COMPOSITIONS AND METHODS FOR CONTROLLING HEAD BLIGHT DISEASE
INCORPORATION OF SEQUENCE LISTING
The materialin the accompanying Sequence g is hereby incorporated by
reference in its entirety. The accompanying file, named “SG11520—1WO_ST25.txt”, was
created on July 24, 2012 and is 55 Kb. The file can be accessed using Microsoft Word on a
er that uses Window OS.
FIELD OF THE INVENTION
The present invention relates to the biological control of phytopathogenic diseases.
Specifically, it relates to compositions and methods useful for controlling head blight disease
in cereal , such as Wheat and barley.
BACKGROUND OF THE ION
Head blight, also known as head scab, pink mold, Whiteheads and tombstone scab,
is a devastating disease ing wheat, barley, and several other cereal crops ide,
ularly in USA, Europe and China. This disease can reach epidemic levels and cause
extensive damage to grains, especially wheat and barley in humid and semi-humid cereal
growing areas of the world, ing India, Russia, France, Germany, and the United
Kingdom. Particularly, wheat scab or head blight is one of the more damaging es of
wheat in the United States. Nationwide, this e has caused the Wheat industry millions
of dollars in yield losses. In the Midwest and High Plains, wheat scab is the major obstacle to
wheat production in recent years. Head blight in addition to attacking Wheat also attacks and
reproduces on barley, oats, corn, and many other cereals.
This serious plant disease can be caused by several phytopathogens, but primarily
by several s in the flmgal genus Fusarz'um. For example, causal agents of the head
blight disease in wheat include a number of different Fusarium species, e. g. F. culmorum, F.
graminearum (teleomorph, Gibberella zeae), F. eum (teleomorph, G. avenacea), F.
poae, as well as by non-Fusarium pathogens such as Microdochium nivale (teleomorph,
Monographella nivalz's), and Microdochium majus. In the United States, Europe and most
agronomically important areas of the world, the predominant causative agent of head blight is
Fusarium graminearum (teleomorph, Gibberella zeae sensu strict).
These pathogens typically survive on plant debris. They invade and damage the
spikelets of the grain head during flowering, thus preventing or lly impeding the
development of grain in the grain head. As a result, the invading scab pathogen can either
kill part of the grain head or the entire grain head. Some infected seeds are low in vigor and
often fail to germinate. Infected seeds that germinate often die early in the ng stage due
to crown rot or root rot, g poor stands in the following crop plant. Healthy seedlings
can also become infected at emergence. In addition to poor, unthrifty stand, yield losses due
to pathogen infestation can be quite high if conditions are favorable for development of the
disease.
The fungal pathogens ofFusarz‘um genus spread across grain cultivating areas all
over the world, and are known to cause severe damage, particularly in areas With high rainfall
between flowering and grain filling. When Fusarium graminearum is the causative agent,
this e is of primary concern because it does not only reduce the cial values of
the contaminated grains, in addition to yield losses, but because Fusarium infection can also
lead to the accumulation oftrichothecene mycotoxins in the grains thus threatening the health
ofhuman and livestock. Trichothecenes are major mycotoxin contaminants of cereals
worldwide, causing feed refusal, vomiting, ea and weight loss in non-ruminant s
and posing a health threat to other s and humans when exposure levels are high. This
threat has been exacerbated by the recent shift in the F. graminearum strains in the United
States towards greater toxin production and vigor. Most ntly found mycotoxins are
deoxynivalenol (DON, also known as vomitoxin) and zearalenone (ZEA). Deoxynivalenol in
ular is a very dangerous toxin, causing gastrointestinal disorders accompanied by
hemorrhagic conditions and the like in humans and animals that eat infected grains, leading
to death in some cases. Since deoxynivalenol is generally stable against changes in pH and
high ature, detoxification can be very difficult. Therefore, grains contaminated
beyond a certain level cannot be used in any form ofbrewing, processing, or livestock feed,
and thus often need to be disposed of.
To date, various strategies have been deployed for controlling head blight in crop
plants. Promising options include chemical measures, the development of resistant crop
ars, and traditional practices of crop rotation and tillage of fields. Among these s,
chemical pesticides can be somewhat effective in reducing head blight infestation, but residue
concerns regarding the use of fungicides late in crop development, typically at flowering
stages only a few weeks before harvest, lessen their attractiveness. Advances in developing
resistant cultivars using traditional breeding and genetic engineering represent another
disease control alternative are also occurring. Reported examples of c engineering
advances include altering the production of a plant hormone or manipulating the plant
hormone ing pathway. In recent years, considerable advances in the area of traditional
breeding have been made in understanding the genetic basis of resistance to head blight
disease and a number of genes and quantitative trait loci (QTL) conferring resistance have
been reported. However, progress in improving crop resistance to head blight disease has
been slow, largely because ofthe difficulty of studying this disease. In fact, relatively little is
currently tood about the mechanisms involved in resistance or susceptibility. In
addition, the c diversity ofFusarz'um species, which are the predominant ive
agents of the disease, often raises concerns regarding how durable the efficacy of chemical
ides and resistant cultivars will be. As a result, practically all wheat cultivars currently
in large-scale production remain vulnerable to infection.
In addition, although some success in controlling head blight disease can be
expected by traditional practices such as plowing fields to bury crop residues infested with
causative agent, 6. g. F. gramz'nearum, after t, conventional tillage of fields after
harvesting is not compatible with the soil conservation practice mum tillage.
Considering the ial of long distance inoculum dispersal and the diverse crops that can
act as alternative hosts of the pathogens, crop rotation is often an ble solution. In
addition to the problem of pesticide residues in the environment, reports of pesticide
ance and instances ofDON t increases in grain can also be concerns with their
use. Further, costs and increasing concerns in the public and private sectors over pesticide
residues in the environment and food product safety render this disease control alternative
less attractive, and have led to requests for crop cultivation using as little ides as
possible.
In summary, despite considerable advances in developing techniques to control
head blight, reducing the impact of this devastating disease on grain production and quality
remains an intractable problem. ore, identification and development ofnew head
blight controlling ques is essential in improving the tion and quality ofmany
cereal crops. These problems require urgent solution not only in United States, but also
across the globe, including the Asia and Europe.
ical control ofhead blight disease has attracted considerable interest since
the mid . Biological control agents (BCAs), though currently very limited in ,
could be an environmentally acceptable method for ntially decreasing the level of
disease incited by ens such as um. Public acceptance, compatibility with other
disease management measures, and durability are among favorable factors in support of
developing strategies for ically controlling head blight disease. ical control
agents could play an important role in organic cereal production. In conventional tion,
such agents may extend protection of spikes past the flowering stage after chemical
fungicides can no longer be applied. To date, significant advances in the area of biological
control have been ed. For example, certain strains of spore-producing bacteria (such as
Bacillus and Pseudomonas species) and yeasts (such as Cryptococcus species) show some
promise for the control of head blight disease and the ion of mycotoxin contamination.
However, despite these and other advances, the need s for improved microorganisms
for use in the biological control of head blight disease. Although BCAs have become a more
acceptable solution for plant pathogens and BCA products have been marketed to a greater
extent than ever before, to date there have been few attempts to develop gies and
nistic microorganism for biologically controlling head blight disease. Furthermore, the
life cycle ofFusarz'um spp. and other causative agents of head blight disease suggest that the
pathogens can potentially be susceptible to biocontrol techniques using antagonistic
microorganisms at different developmental stages. Thus, there is a need to identify new
biological control agents, preferably with ent modes of actions, as well as biocontrol
methods that can help effectively prevent or suppress the development ofhead blight disease.
SUMMARY OF THE INVENTION
Compositions comprising microbiological strains and cultures are provided herein.
Certain strains, cultures, and itions thereof are useful for the control of head blight
disease, for example, of various crop plants including wheat and other cereal plants.
Biological control compositions, and methods ofuse thereof to prevent, inhibit or treat the
development of plant pathogens or disease and for preserving plant yield, are also provided.
Also provided are methods for the use of such compositions as biological control agents in
ation with other agriculturally effective compounds or compositions for controlling
l plant pathogens.
In one aspect, the present invention provides isolated microbial strains having
suppressive activity against head blight disease. The microbial strains in accordance to this
aspect of the present invention are selected from the group consisting of the genera
Microbacterium, Bacillus, Mycosphaerella, and Variovorax. In some preferred
embodiments, the microbial strains are selected from the group consisting of Mycosphaerella
sp. strain SGI H11 (deposited as NRRL 50471), Microbacterium sp. strain SGI
C06 (deposited as NRRL B-50470), Microbacterium sp. strain SGIG08, Variovorax sp.
strain SGIG01 (deposited as NRRL B-50469), us sp. strain SGIF03
(deposited as NRRL B-50760), Bacillus sp. strain SGIH06 (deposited as NRRL B-
50761), and pesticidally active variants of any thereof. T he microbial strain in accordance to
some other preferred embodiments can comprise a DNA sequence that exhibits at least 85%
sequence identity to any one of the nucleotide sequences in the Sequence Listing. r
provided are biologically pure es and enriched cultures of the microbial strains
disclosed .
Also provided in another aspect of the present invention are itions that
se a microbial strain of the invention or a culture thereof, and an agriculturally
effective amount of a compound or composition selected from the group consisting of an
acaricide, a bactericide, a ide, an insecticide, a microbicide, a nematicide, a pesticide,
and a fertilizer. The compositions in some embodiments of this aspect may be prepared as a
formulation selected from the group consisting of an emulsion, a colloid, a dust, a granule, a
pellet, a , a spray, an emulsion, and a solution. In some other embodiments, the
compositions may be provided with a carrier. In some preferred embodiment, the r is
an agriculturally acceptable carrier. In some particularly preferred embodiment, the carrier is
a plant seed. In other preferred ments, the composition is a seed coating ation.
Further ed in the present disclosure are seeds that are coated with a composition
according to the present invention.
In another aspect of the present invention, there are provided s for
preventing, inhibiting or treating the development of a plant pathogen. T he methods involve
growing a microbial strain of the invention or a culture thereof in a growth medium or soil of
2012/048012
a host plant prior to or concurrent with host plant growth in the growth medium or soil. In
some preferred embodiments of this aspect, the plant pathogen causes head blight disease. In
some particularly preferred ments, the plant en is Fusarium graminearum.
In yet another aspect ofthe present invention, methods are provided for preventing,
inhibiting or treating the development of head blight e of a plant. The methods e
applying to the plant, or to the plant's surroundings, an effective amount of a microbial strain
ofthe invention or a culture thereof. In one embodiment, such head blight disease is caused
by the fungus Fusarz'um gramz’nearum. In some embodiments ofthis aspect, the microbial
strain or a culture thereof is d to soil, a seed, a root, a flower, a leaf, a portion of the
plant, or the whole plant. In a preferred embodiment, the plant is susceptible to Fusarz'um
graminearum. In some other preferred embodiments, the plant is wheat plant, a corn plant, a
barley plant, or an oat plant. In another preferred embodiment, the ial strain of the
present invention or a culture thereof is established as an endophyte on the plant.
Another further aspect of the invention provides non-naturally occurring plants.
The non-naturally occurring plants are artificially infected with a ial strain of the
invention or a culture thereof. Further provided in some red embodiments of this
aspect are seed, uctive tissue, vegetative tissue, plant parts, and progeny of the non-
naturally occurring plants.
Yet another aspect of the invention provides a method for preparing an agricultural
composition. The method involves inoculating the microbial strain according to the present
invention or a culture thereof into or onto a substratum and allowing it to grow at a
temperature of 1-37°C until obtaining a number of cells or spores of at least 102-103 per
milliliter or per gram.
These and other objects and features of the invention will become more fully
apparent from the following detailed description of the invention and the claims.
DETAILED DESCRIPTION OF THE ION
Some definitions
Unless otherwise defined, all terms of art, notations and other scientific terms or
ology used herein are ed to have the meanings commonly understood by those of
skill in the art to which this invention pertains. In some cases, terms with commonly
understood meanings are defined herein for clarity and/or for ready reference, and the
inclusion of such definitions herein should not necessarily be construed to represent a
substantial difference over what is generally understood in the art. Many of the techniques
and procedures described or referenced herein are well understood and commonly employed
using conventional methodology by those skilled in the art.
The singular form “a”, “an”, and “the” include plural references unless the context
y dictates otherwise. For example, the term “a cell” includes one or more cells,
including mixtures thereof. By "comprising" is meant including, but not limited to, er
follows the word "comprising".
The expressions onistic microorganism” and “microbial antagonist” are used
herein interchangeably in reference to a microorganism is intended to mean that the subject
strain exhibits a degree of inhibition of head blight disease exceeding, at a statistically
significant level, that of an ted control.
Antibiotic: the term “antibiotic”, as used herein, refers to any substance that is able
to kill or inhibit the growth of a microorganism. Antibiotics may be produced by any one or
more of the following: 1) a microorganism, 2) a synthetic process, or 3) a semisynthetic
process. An antibiotic may be a microorganism that secretes a volatile organic compound.
Furthermore, an antibiotic may be a volatile organic compound secreted by a microorganism.
icidal: the term “bactericidal”, as used herein, refers to the ability of a
composition or substance to increase mortality or inhibit the growth rate of bacteria.
Inhibition of the growth rate of bacteria can be commonly quantified as the reduction of
viable bacterial cells over time.
Biological control: the term “biological control” and its abbreviated form
“biocontrol”, as used , is d as control of a pathogen or insect or any other
rable sm by the use of at least a second organism other than man. An example
of a known mechanism ofbiological control is the use of microorganisms that control root rot
by out-competing fungi for space on the surface of the root, or rganisms that either
inhibit the growth of or kill the pathogen. The “host plant” in the t of biological
control is the plant that is tible to disease caused by the pathogen. In the context of
ion of an organism, such as a fungal species, from its natural environment, the “host
plant” is a plant that supports the growth ofthe fungus, for example, a plant of a species the
fungus is an endophyte of.
The term "cereal" as used herein is intended to refer to any cereal species that can
be susceptible to head blight disease. Cereals reported to be susceptible include wheat,
barley, oats, and triticale, though wheat and barley are the two crops in which this disease
presents a significant economic problem.
An "effective amoun " refers to an amount ent to affect beneficial or desired
results. In terms of e management, treatment, inhibition or protection, an effective
amount is that amount sufficient to suppress, stabilize, reverse, slow or delay progression of
the target infection or e states. As such, the expression “an effective amoun ” is used
herein in reference to that quantity of antagonist treatment which is necessary to obtain a
reduction in the level of pathogen development and/or in the level of pathogenic disease
relative to that ing in an untreated control. Typically, an effective amount of a given
antagonist treatment provides a reduction of at least 20%; or more typically, between 30 to
40%; more typically, n 50—60%; even more typically, between 70 to 80%; and even
more typically, between 90 to 95%, relative to the level of e and/or the level of
pathogen development occurring in an untreated control under suitable conditions of
treatment. An effective amount can be administered in one or more administrations. The
actual rate of application of a liquid ation will usually vary from a minimum of about 1
X 103 to about 1 X 1010 Viable cells/mL and preferably from about 1 X 106 to about 5 X 109
Viable cells/mL. Under most conditions, the antagonistic microbial s ofthe ion
described in the Examples below, would be optimally effective at application rates in the
range of about 1 X 106 to l X 109 Viable cells/mL, assuming a mode of application which
would achieve substantially uniform contact of at least about 50% of the plant tissues. If the
antagonists are applied as a solid formulation, the rate of application should be controlled to
result in a able number of viable cells per unit area ofplant tissue surface as obtained
by the aforementioned rates of liquid ent. Typically, the biological control agents of
the present ion are biologically effective when delivered at a concentration in excess of
106 CFU/g (colony forming units per gram), preferably in excess of 107 CFU/g, more
preferably 108 CFU/g, and most preferably at 109 CFU/g.
Further, the sion "effective microbial antagonist" used herein in nce to
a microorganism is intended to mean that the subject microbial strain exhibits a degree of
tion of head blight disease exceeding, at a statistically cant level, that of an
untreated control. Typically, an effective microbial antagonist has the ability to effect a
reduction of at least 20%; or more typically, between 30 to 40%; more typically, between 50-
60%; even more typically, between 70 to 80%; and even more typically, between 90 to 95%,
relative to the level of disease and/or the level ofpathogen development occurring in an
untreated control under suitable conditions of treatment.
Composition: A “composition” is intended to mean a combination of active agent
and at least another compound, carrier or composition, inert (for example, a detectable agent
or label or liquid carrier) or active, such as a pesticide.
Isolated microbial strain, isolated culture, biologically pure culture, and enriched
culture: As used herein, the term “isolated” as applied to a microorganism (e.g., bacterium or
microfungus) refers to a microorganism which has been removed and/or purified from an
environment in which it naturally occurs. As such, an “isolated strain “of a microbe as used
herein is a strain that has been removed and/or purified from its natural milieu. Thus, an
“isolated microorganism” does not include one residing in an environment in which it
naturally occurs. Further, the term ted" does not necessarily reflect the extent to which
the e has been d. A "substantially pure culture" of the strain of microbe refers
to a culture which contains ntially no other microbes than the desired strain or strains
of microbe. In other words, a ntially pure culture of a strain of microbe is substantially
free of other contaminants, which can e microbial contaminants as well as undesirable
chemical contaminants. Further, as used herein, a "biologically pure" strain is intended to
mean the strain separated from als with which it is normally associated in nature. Note
that a strain associated with other strains, or with compounds or materials that it is not
normally found with in , is still defined as "biologically pure." A monoculture of a
particular strain is, of course, "biologically pure." As used herein, the term "enriched culture"
2012/048012
of an ed ial strain refers to a microbial culture that contains more than 50%, 60%,
70%, 80%, 90%, or 95% of the isolated strain.
As used herein, an "endophyte" is an endosymbiont that lives within a plant for at
least part of its life Without causing apparent disease. Endophytes may be transmitted either
vertically (directly from parent to offspring) or horizontally (from individual to unrelated
individual). Vertically-transmitted fungal endophytes are typically asexual and transmit from
the maternal plant to offspring via fungal hyphae penetrating the host's seeds. Bacterial
endophytes can also be transferred vertically from seeds to seedlings (Ferreira et al., 2008).
Conversely, horizontally-transmitted endophytes are typically sexual, and transmit via spores
that can be spread by Wind and/or insect vectors. Endophytes of crop plants have been
receiving considerable attention with t to their ability to control both disease and insect
infestation, as well as promoting plant growth.
onally comparable protein: The phrase “functionally comparable n” as
used herein describes those proteins that have at least one characteristic in common. Such
characteristics include sequence similarity, biochemical activity, transcriptional pattern
similarity and ypic activity. Typically, the functionally comparable proteins share
some ce similarity or at least one biochemical. Within this definition, homologs,
orthologs, paralogs and analogs are considered to be functionally comparable. In addition,
functionally comparable proteins generally share at least one biochemical and/or phenotypic
activity. Functionally comparable ns will give rise to the same characteristic to a
similar, but not necessarily the same, degree. Typically, functionally comparable proteins
give the same characteristics where the quantitative measurement due to one ofthe
comparables is at least 20% of the other; more typically, between 30 to 40%; more lly,
between ; even more typically, between 70 to 80%; even more typically, between 90
to 95%; even more typically, between 98 to 100% ofthe other.
Fungicidal: As used herein, “fungicidal” refers to the ability of a composition or
substance to decrease the rate of growth of fimgi or to increase the ity of fimgi.
Fusarz'um fungus: For purposes of this ion it is understood that the use of
term Fusarium fimgus is intended to include both the sexual (teleomorphic) stage of this
organism and also the asexual rphic) stage, also referred to as the perfect and
imperfect fungal , respectively. For example, the anamorphic stage ofFusarium
graminearum is ella zeae, a causative agent ofhead blight disease. This disease
typically occurs when the flower or seed head becomes inoculated with conidia produced by
the imperfect form or ascospores produced by the perfect form of this fimgus.
Mutant: As used herein, the term “mutant” or “varian ” in reference to a
microorganism refers to a modification ofthe parental strain in which the desired biological
activity is similar to that expressed by the parental strain. For example, in the case of
Mcrobacterium the “parental strain” is defined herein as the original Microbacz‘erium strain
before mutagenesis. s or ts may occur in nature without the intervention of
man. They also are obtainable by treatment with or by a variety of methods and
compositions known to those of skill in the art. For example, a parental strain may be treated
with a chemical such as N-methyl-N'-nitro-N—nitrosoguanidine, ethylmethanesulfone, or by
irradiation using gamma, X-ray, or UV-irradiation, or by other means well known to those
practiced in the art.
Nematicidal: The term “nematicidal”, as used , refers to the ability of a
substance or composition to increase mortality or inhibit the growth rate of nematodes.
Pathogen: The term gen" as used herein refers to an organism such as an
alga, an arachnid, a bacterium, a fungus, an insect, a nematode, a parasitic plant, yeast, a
protozoan, or a virus capable of producing a disease in a plant or animal. The term
"phytopathogen" as used herein refers to a pathogenic organism that infects a plant.
Percentage of percent ty: “percentage of sequence ty”, as used herein, is
determined by comparing two lly locally aligned ces over a comparison
Window defined by the length of the local alignment between the two sequences. The amino
acid sequence in the comparison window may comprise additions or deletions (e. g., gaps or
overhangs) as compared to the reference sequence (which does not comprise ons or
deletions) for l alignment of the two sequences. Local alignment between two
ces only includes segments of each sequence that are deemed to be sufficiently similar
according to a criterion that depends on the algorithm used to perform the alignment (6. g.
BLAST). The percentage identity is calculated by determining the number of ons at
which the identical nucleic acid base or amino acid residue occurs in both sequences to yield
the number of matched positions, dividing the number ofmatched ons by the total
number of positions in the window of comparison and lying the result by 100. Optimal
alignment of sequences for comparison may be ted by the local homology algorithm
of Smith and Waterman (1981) Add. APL. Math. 2:482, by the global homology alignment
algorithm ofNeedleman and Wunsch (J. Mol. Biol. 48:443, 1970), by the search for
similarity method of Pearson and Lipman (Proc. Natl. Acad. Sci. USA 85: 2444, 1988), by
tic implementations of these algorithms (NCBI BLAST, WU-BLAST, BLAT, SIM,
BLASTZ), or by tion. Given that two sequences have been identified for comparison,
GAP and BESTFIT are preferably employed to determine their optimal alignment.
lly, the default values of 5.00 for gap weight and 0.30 for gap weight length are used.
The term “substantial sequence identity” between polynucleotide or polypeptide sequences
refers to polynucleotide or polypeptide comprising a sequence that has at least 50% sequence
identity, preferably at least 70%, preferably at least 80%, more preferably at least 85%, more
preferably at least 90%, even more preferably at least 95%, and most preferably at least 96%,
97%, 98% or 99% sequence identity compared to a reference sequence using the programs.
Query c acid and amino acid sequences can be searched t subject
nucleic acid or amino acid sequences residing in public or proprietary databases. Such
searches can be done using the National Center for Biotechnology Information Basic Local
Alignment Search Tool (NCBI BLAST v 2.18) program. The NCBI BLAST program is
ble on the intemet from the National Center for Biotechnology Information
.ncbi.nlm.nih.gov/Blast.cgi). Typically the following ters for NCBI BLAST can
be used: Filter options set to "default”, the Comparison Matrix set to "BLOSUM62”, the Gap
Costs set to “Existence: 11, Extension: 1”, the Word Size set to 3, the Expect (E threshold)
set to 16-3, and the minimum length of the local alignment set to 50% of the query sequence
length. Sequence identity and similarity may also be determined using GenomeQuestTM
software (Gene-IT, Worcester Mass. USA).
The term “pesticidal”, as used herein, refers to the ability of a substance or
composition to decrease the rate of growth of a pest, i.e., an red organism, or to
increase the mortality of a pest.
By “suppressive activity” of a biological control agent against a phytopathogen is
meant the ability of the agent to suppress, inhibit, stabilize, reverse, slow, or delay the
development ofthe pathogen itself, or the progression of the infection or disease states
caused by the pathogen.
Variant: A “varian ”, as used herein in reference to a microorganism, is a strain
having identifying characteristics of the species to which it belongs, While having at least one
nucleotide sequence variation or fiably different trait with respect to the parental strain,
where the trait is genetically based (heritable). For e, for a Microbacterium sp. SGI-
SGI—Ol4-CO6 strain having fungicidal activity, identifiable traits include 1) the ability to
suppress the growth ofFusarium graminearum and its teleomorph Gibberella zeae; 2) the
ability to suppress the development of head blight disease; 3) having housekeeping genes
with greater than 95%, greater than 96%, greater than 97%, greater than 98%, or greater than
99% sequence identity to the housekeeping genes ofMicrobacterz'um sp. SGI-Ol4-CO6 can be
used to confirm a variant as Microbacterium sp. 4-C06.
For nucleic acids and polypeptides, the term “varian ” is used herein to denote a
ptide, protein or polynucleotide molecule with some differences, generated
synthetically or naturally, in their amino acid or nucleic acid sequences as compared to a
reference ptide or polynucleotide, respectively. For example, these differences include
substitutions, insertions, deletions or any desired ations of such changes in a reference
or ptide.
, polypeptide Polypeptide and protein variants can further consist of changes
in charge and/or post-translational ations (such as glycosylation, methylation,
phosphorylation, etc.)
All publications and patent applications mentioned in this specification are herein
incorporated by reference to the same extent as if each individual publication or patent
application was specifically and individually indicated to be incorporated by reference.
No ion is made that any reference constitutes prior art. The discussion of
the references states What their authors assert, and the applicants reserve the right to
challenge the cy and ence of the cited documents. It will be clearly tood
that, although a number of prior art publications are referred to herein, this reference does not
tute an admission that any of these documents forms part of the common general
knowledge in the art.
2012/048012
Methods for Taxonomic Identification
Microorganisms can often be distinguished based on direct microscopic analysis
(do all of the cells in a sample look the same on examination), staining characteristics, simple
molecular is (such as a simply restriction fiagment length polymorphism (RFLP)
ination), and so forth. In addition to the illustrative examples of such taxonomic
analysis techniques as described at Examples 2-3 of the present disclosure, taxonomic
identification of a microorganism can e up to several different levels of analysis, and
each analysis can be based on a different characteristic of the organism. Such taxonomic
analyses can include nucleic acid-based analysis (e.g., analysis of individual specific genes,
either as to their presence or their exact sequence, or expression of a ular gene or a
family of genes), protein-based analysis (e. g. , at a fimctional level using direct or indirect
enzyme assays, or at a structural level using irnmuno—detection techniques), and so forth.
a. Nucleic acid-based analysis: One of ordinary skill in the art will appreciate that a
wide variety of nucleic acid-based techniques are known and can be useful in ing the
taxonomic identification of a given microorganism. These techniques can be used to identify
cells by gene sequence or to identify cells that have particular genes or gene families.
Common gene families useful for taxonomic studies e 168 gene family, actin gene
family, and inase A (recA) gene family. These methods typically e amplifying
and sequencing genes from very small numbers of cells, and therefore often overcome the
problems of concentrating cells and their DNA from dilute suspensions. The term “nucleic
acid amplification" generally refers to techniques that increase the number of copies of a
nucleic acid molecule in a sample or specimen. Techniques useful for nucleic acid
amplification are well known in the art. An example of nucleic acid amplification is the
rase chain reaction (PCR), in which a biological sample collected from a subject is
contacted with a pair of ucleotide primers, under conditions that allow for the
hybridization of the primers to nucleic acid template in the sample. The primers are extended
under suitable ions, dissociated fi'om the te, and then re-annealed, extended, and
dissociated to y the number of copies of the nucleic acid. Other examples of in vitro
amplification techniques include strand displacement amplification; transcription-free
isothermal amplification; repair chain reaction amplification; ligase chain reaction; gap filling
ligase chain reaction amplification; coupled ligase detection and PCR; and RNA
transcription-free amplification.
In addition to the illustrative example primers provided herein, see, e.g. Examples
2-3 and the Sequence Listing, primers have also been designed ely, and new ones are
ually being designed, for individual species or phylogenetic groups of microorganisms.
Such narrowly targeted primers can be used with the methods described herein to screen
and/or identify specifically only the microorganisms of interest.
Methods for preparing and using nucleic acid primers are described, for example,
in Sambrook et al. (In lar Cloning: A Laboratory Manual, CSHL, New York, 1989),
Ausubel et al. (ed.) (In Current Protocols in Molecular y, John Wiley & Sons, New
York, 1998). Amplification primer pairs can be derived from a known sequence, for
example, by using computer programs intended for that purpose such as Primer (Whitehead
Institute for ical Research, Cambridge, Mass). One of ry skill in the art will
appreciate that the specificity of a particular probe or primer increases with its length. Thus,
for example, a primer comprising 30 consecutive nucleotides of an rRNA-encoding
tide or flanking region thereof will anneal to a target sequence With a higher specificity
than a corresponding primer of only 15 nucleotides. Thus, in order to obtain greater
specificity, probes and s can be selected that comprise at least 20, 25, 30, 35, 40, 45, 50
or more consecutive tides of a target tide sequence such as the 168 rRNA.
Common techniques for the preparation of nucleic acids useful for nucleic acid
applications (6. g. , PCR) include phenol/chloroform tion or use of one of the many
DNA extraction kits that are available on the market. Another way that DNA can be
amplified is by adding cells directly to the c acid amplification reaction mix and relying
on the denaturation step of the amplification to lyse the cells and release the DNA.
The product ofnucleic acid amplification reactions may be further characterized by
one or more of the standard techniques that are well known in the art, including
electrophoresis, restriction endonuclease cleavage patterns, oligonucleotide ization or
ligation, and/or nucleic acid sequencing. When in hybridization techniques are used for cell
identification purposes, a variety ofprobe labeling methods can be useful, including
cent labeling, radioactive labeling and non-radioactive labeling. When nucleic acid
sequencing techniques are used, homology search for the nucleotide sequence of the
amplified nucleic acid molecules can be conducted using various ses ofknown
sequences, including but not d to DDBJ/GenBank/EMBL databases.
b. Protein—based analysis: In addition to analysis of nucleic acids, microorganisms
can be mically characterized and identified based on the presence (or absence) of
specific proteins directly. Such analysis can be based on the activity of the specified protein,
e. g.
, through an enzyme assay or by the response of a co-cultured organisms, or by the mere
presence ofthe specified n (which can for instance be determined using immunologic
methods, such as in situ immunofluorescent antibody staining).
Enzyme assays: By way of example, fluorescent or chromogenic ate analogs
can be included into the growth media (e.g. microtiter plate cultures), followed by incubation
and screening for reaction products, thereby identifying cultures on a basis of their enzymatic
activities.
Co-cultivation se: In some embodiments of the present invention, the
activity of an enzyme carried by a microbial isolate can be assayed based on the response (or
degree of response) of a co-cultured organism (such as a reporter organism).
A variety ofmethods can also be used for identifying microorganisms selected and
isolated from a source nment by binding at least one antibody or antibody—derived
le to a molecule, or more ularly an epitope of a molecule, ofthe microorganism.
Antijrrricroorganism protein antibodies may be produced using standard
procedures described in a number of texts, including Harlow and Lane (Antibodies, A
Laboratory Manual, CSHL, New York, 1988). The determination that a particular agent
binds substantially only to a protein of the desired microorganism may readily be made by
using or adapting routine ures. One suitable in vitro assay makes use of the Western
blotting procedure (described in many standard texts, including Harlow and Lane
(Antibodies, A tory Manual, CSHL, New York, 1988)).
r fragments of antibodies (antibody-derived molecules, for instance, FAbs,
Fvs, and single-chain Fvs (SCFvs)) can also serve as c binding agents. Methods of
making these fragments are routine.
ion of antibodies that bind to cells on an array ofthis invention can be
carried out using standard techniques, for instance ELISA assays that e a detectable
signal, for instance a fluorescent or scent signal.
Isolated cultures of the invention
As described in more details in the Examples section of the present disclosure,
Applicants have discovered several agriculturally beneficial novel microorganisms, for
example, effective suppressors ofhead blight disease. ularly, these novel antagonistic
microorganisms are ive for reduction of head blight severity and for inhibition of the
growth ofFusarium graminearum, a primary ive agent of head blight disease in wheat.
The microbial antagonists were identified from a pool of approximately 5,000 microbial
strains obtained from Wild plant samples collected from l locations in the United States.
Initial selection of antagonistic microorganism was based on the ability of the
microorganisms to suppress the development of F. graminearum pathogen and that of its
teleomorph Gibberella zeae in an in vitro antagonism assay. Selected microbial antagonists
were then bio-assayed in a greenhouse study on wheat ngs, which involved inoculation
of the ngs with the microbial strains, followed by repeated ations of F.
graminearum , for the ability of the microbial s to reduce the severity of fungal
infestation and for their ability to ve seed yield. The antagonistic microorganisms
selected in this manner were found to be effective in reducing the severity of head blight in
greenhouse trials.
Taxonomic analysis further determined that each ofthe antagonistic
microorganisms described in the present disclosure are closely related either the bacterial
genus Microbacterium, the bacterial genus Bacillus, the bacterial genus Variovorax, or the
fungus genus Mycosphaerella.
The genus Microbacterium, the type genus of the family Microbacteriaceae, is
generally ered to accommodate Gram—positive, non-spore forming, rod-shaped bacteria
that were originally ed during early studies on lactic acid-producing bacteria. Members
ofthe genus Microbacterium are originally characterized largely by their marked heat
resistance, presence in dairies, and production of small amounts of I..(+) lactic acid from
glucose. In contrast to other genera of the family Microbacterz'aceae in which species are
characterized by a coherent peptidoglycan type, species ofMicrobacterium possess omithine
or lysine either in the inter-peptide bridge or at position 3 of B-type peptidoglycan. In other
chemotaxonomic properties, such as isoprenoid quinones (MK-l l, MK-12, , polar
lipids, fatty acids and base composition of DNA, members of the genus exhibit the usual
range of diversity found in other genera of Microbacteriaceae. Two bacterial genera
Microbacterium and Aureobacterz'um can be united according to some taxonomy studies. To
date, members ofthe genus acterium comprise at least 33 s, which have been
isolated from a broad range of habitats, including soil, dairy products, plant galls, insects or
clinical specimens. Various aspects of their ecology, phylogeny, taxonomy, culture methods,
and long-term preservation conditions have recently been summarized by Evtushenko and
Takeuchi (2006). One of skill in the art will readily appreciate that microorganism of the
genus acterium can be taxonomically identified y by any ofthe taxonomic
identification techniques described above, including the chemotaxonomic analysis of the cell
wall peptidoglycan and comparative 16S rDNA sequence analysis as described in
Evtushenko and Takeuchi (2006) and references cited therein, as well as in those described in
Examples 2-3 ofthe present disclosure. As discussed in detail below, to date l
naturally occurring rganisms have been ed as having antagonistic activity
against head blight disease. r, there are no reports prior to the present invention that
be a microorganism ofthe genus Mycobacterium having such antagonistic activity.
Further, prior to the t ion, the present inventors were not aware of any s
or processes of using a bacterial strain of the genus Mycobacterz'um as trol agent in
preventing, inhibiting or treating the development of a causative pathogen of head blight
disease.
The genus Bacillus is a genus of Gram-positive/variable, spore-forming, rod-
shaped bacteria. Similarly to other genera associated with the early history of microbiology,
such as Pseudomonas or Vibrz’o, nearly 266 species members of the Bacillus genus are found
ubiquitously, and it is widely considered to be one of the genera with the largest 168 diversity
and environmental diversity. Bacillus species can be obligate aerobes or facultative
anaerobes, and test positive for the enzyme catalase. Ubiquitous in nature, Bacillus includes
both free—living and pathogenic species. Under stressful environmental conditions, the cells
produce oval endospores that can stay dormant for extended periods. These characteristics
originally defined the genus, but not all such species are closely related, and many have been
moved to other . In fact, several studies have tried to reconstruct the phylogeny of the
genus. The Bacillus-specific study with the most diversity covered is by Xu and Cote [Int]. J
ofSyst. Evol. Microbiol. 53 (3): 695—704; 2003], using 16S and the ITS region, where they
divide the genus into 10 groups, which includes the nested genera Paenibacillus,
Brevibacillus, Geobacillus, Marinibacillus and Virgibacillus. However, according to more
recent studies, the genus Bacillus contains a very large number of nested taxa and especially
in both 168 and 23S it is considered to be paraphyletic to Lactobacillales (Lactobacillus,
Streptococcus, lococcus, Listeria, eta), due to Bacillus coahuilensis and others (see,
e. g., Yarda et al., Syst. Appl. Microbiol. 31 (4): 241—250, 2008; Yarda et al., Syst. Appl.
Microbiol. 33 (6): 291—299, 2010]. One particular clade, formed by B. anthracis, B. cereus,
B. mycoz'des, B. pseudomycoz'des, B. gz‘ensis and B. weihenstephanensis under current
classification standards, should be a single species (within 97% 168 identity), but due to
medical reasons, they are considered separate species. In addition to the taxonomy is
methods described at Examples 2-3 ofthe present disclosure, the phylogenetic and taxonomic
analyses ofBacillus species can be performed by a variety oftechniques, including those
discussed in s in Xu and Cote, 2003; Yarda ez‘ al., 2008; Yarda et al., 2010..
The genus Variovorax was originally created by reclassification ofAlcaligenes
paradoxus as Variovorax paradoxus (Willems er al., 1991), which is widely consider as the
type species of this genus. V. xus has been extensively studied as a model for novel
biodegradation agents, as well as microbe/microbe and microbe/plant interactions. Other
s include V. ensis, V. soli (Kim et al., 2006), and V. borom’cumulans (Miwa et
al., 2008). Variovorax species are catabolically very diverse and engage in mutually
beneficial interactions with other ial species in many biodegradations, and therefore
s ecological importance and high application potential. For example, a soil
methanotroph, only when tured together with a V. paradoxus strain, exhibits high
affinity for methane (a potent greenhouse gas), and this trait is not y observed in
laboratory es. Similarly, a close relative of Variovorax has been found to be the central,
non—photosynthetic partner within the phototrophic consortium "Chlorochromatz'um
aggregatum.” Some species of the genus orax also have the ability to interfere with the
communication of other bacteria. Some yet other species of the genus Variovorax can
intimately interact with other biota (e.g. , plants) in various ecosystems. Moreover, some
Variovorax species, residing in the area just outside plant roots and/or inside a plant, have
been reported for being capable of promoting plant growth via the reduction of ethylene
levels, the repression of quorum-sensing-controlled enesis, and the increase of
resistance to heavy metals, which greatly benefits phytoremediation. In addition to the
my analysis methods described at Examples 2-3 ofthe present disclosure, the
phylogenetic and taxonomic analyses of Variovorax species can be performed by a variety of
techniques, including those discussed in details elsewhere herein.
haerella is a very large fiingus genus, with over 2,000 s names and at
least 500 species associated with more than 40 anamorph genera (especially Cercospora,
Pseudocercospora, Septoria, Ramularia, etc). In addition, several thousand phs lack
telomorphs. The genus of Mycosphaerella es species that are pathogens, saprobes,
endophytes, or mutualistic associations. Various aspects of their ecology, phylogeny,
taxonomy, culture methods, and long-term preservation ions have recently been
reported (see, e. g. Crous et al., nia, 23:119-146,2009). One of skill in the art will
readily appreciate that microorganism ofthe genus Mycosphaerella can be taxonomically
fied by any ofthe taxonomic techniques described above, or a ation thereof.
Most common techniques include comparative ce analyses using 16S rDNA sequences
and the internal transcribed spacer regions as described in, for example, Crous et al.
, Studies
in Mycology, 55:235—253,2006; Crous et al., 2009, supra; Goodwin et al., Phytopathology 91:
648—65 8, 2001; and those described in Examples 2—3 of the present disclosure.
Deposit of ical Material
Purified cultures of microbial strains identified as having suppressive activity
against head blight disease were deposited in the Agricultural Research e Culture
Collection located at 1815 N. University Street, Peoria, IL 61604, USA (NRRL) in
accordance with the Budapest Treaty for the purpose nt procedure and the regulations
thereunder (Budapest Treaty). Accession numbers for these deposits are as follows:
N ———
SGI—OlO-Hll NRRL 50471
SGIC06 NRRL 13—50470
SGIG01 llllilNRRL B-50469
SGI-OlS-FO3 NRRL B-50760
SGI-OlS-H06 NRRL B-50761
The microbial s have been deposited under conditions that ensure that access
to the culture will be available during the pendency of this patent application to one
determined by the Commissioner of Patents and Trademarks to be ed thereto under 37
C.F.R. §1.14 and 35 U.S.C. §122. The ts ent substantially pure cultures of the
ted strains. The deposits are ble as ed by foreign patent laws in countries
wherein counterparts of the subject application or its progeny are filed. However, it should
be understood that the availability of a deposit does not constitute a license to practice the
subject invention in derogation of patent rights d by governmental action.
Preferred microorganisms of the present invention have all ofthe identifying
characteristics of the deposited strains and, in ular, the identifying characteristics of
being able to suppress the development of head blight disease as described herein, and as
being able to suppress the development ofFusarz‘um gramz'nearum pathogen and its
teleomorph Gibberella zeae as described herein. In particular, the preferred microorganisms
ofthe present invention refer to the deposited microorganisms as described above, and
mutants thereof.
Microbiological compositions
The microbiological compositions ofthe present invention that se isolated
microbial strains or es thereof can be in a variety of forms, including, but not d to,
still cultures, whole cultures, [stored stocks of cells, mycelium and/or hyphae (particularly
glycerol stocks), agar strips, stored agar plugs in glycerol/water, freeze dried stocks, and
dried stocks such as lyophilisate or mycelia dried onto filter paper or grain seeds. As defined
elsewhere herein, “isolated culture” or grammatical equivalents as used in this disclosure and
in the art is understood to mean that the ed to culture is a culture fluid, pellet, scraping,
WO 16361
dried sample, lyophilate, or section (for e, hyphae or mycelia); or a t, container,
or medium such as a plate, paper, filter, matrix, straw, pipette or pipette tip, fiber, needle, gel,
swab, tube, vial, particle, etc. that contains a single type of organism. In the present
invention, an isolated e of a microbial antagonist is a culture fluid or a scraping, pellet,
dried ation, lyophilate, or n of the microorganism, or a support, container, or
medium that contains the microorganism, in the absence of other organisms.
The present disclosure further provides compositions that contain at least one
isolated microbial strains or cultures thereof of the present invention and a carrier. The
carrier may be any one or more of a number of carriers that confer a variety of properties,
such as increased stability, wettability, dispersability, etc. Wetting agents such as natural or
synthetic surfactants, which can be nonionic or ionic surfactants, or a combination thereof
can be ed in a composition ofthe invention. Water-in—oil emulsions can also be used to
formulate a composition that includes at least one isolated microorganism of the present
invention (see, for example, US. Patent No. 7,485,451, incorporated by reference herein).
Suitable formulations that may be prepared include wettable powders, granules, gels, agar
strips or s, thickeners, and the like, ncapsulated particles, and the like, liquids
such as aqueous flowables, aqueous suspensions, water-in—oil emulsions, etc. The
formulation may e grain or legume products (e.g. or beans, broth or flour
, ground grain
derived from grain or beans), starch, sugar, or oil. The carrier may be an agricultural carrier.
In certain preferred embodiments, the carrier is a seed, and the composition may be applied
or coated onto the seed or d to saturate the seed.
In some embodiments, the agricultural carrier may be soil or plant growth medium.
Other agricultural carriers that may be used include water, fertilizers, plant-based oils,
ants, or combinations thereof. Alternatively, the agricultural r may be a solid,
such as diatomaceous earth, loam, , alginate, clay, bentonite, vermiculite, seed cases,
other plant and animal products, or combinations, including granules, pellets, or sions.
Mixtures of any of the aforementioned ingredients are also contemplated as carriers, such as
but not limited to, pesta (flour and kaolin clay), agar or flour-based pellets in loam, sand, or
clay, etc. Formulations may include food sources for the cultured organisms, such as barley,
rice, or other biological materials such as seed, plant parts, sugar cane bagasse, hulls or stalks
from grain processing, ground plant material (e.g. “yard waste”) or wood from building site
refuse, sawdust or small fibers from recycling of paper, fabric, or wood. Other suitable
formulations will be known to those skilled in the art.
In the liquid form, 6. g. solutions or suspensions, the microorganisms may be mixed
or suspended in water or in aqueous solutions. Suitable liquid diluents or carriers include
water, aqueous solutions, petroleum lates, or other liquid carriers.
Solid compositions can be prepared by dispersing the antagonist microorganisms
in and on an appropriately d solid carrier, such as peat, wheat, bran, vermiculite, clay,
talc, bentonite, diatomaceous earth, fuller's earth, pasteurized soil, and the like. When such
formulations are used as wettable s, biologically compatible dispersing agents such as
non—ionic, anionic, amphoteric, or cationic dispersing and emulsifying agents can be used.
In a preferred embodiment, the compositions contemplated herein prevent attack
by head blight disease upon plants, particularly cereal plants, such as wheat, barley, oat, and
corn and, when used in sufficient amounts, to act as microbial antagonists. These
compositions, similarly to other biocontrol agents, have a high margin of safety because they
typically do not burn or injury the plant.
As bed in great detail throughout the present disclosure, control of head
blight disease may be effected by application of one or more ofthe iological
compositions ofthe present invention to a host plant or parts ofthe host plant. The
compositions can be applied in an amount effective to reduce the level of head blight relative
to that in an untreated control. The active constituents are used in a concentration sufficient
to inhibit plant pathogen pment ofthe targeted plant pathogen when applied to the
cereal plant. As will be apparent to a d person in the art, effective concentrations may
vary depending upon such factors as: (a) the type of the plant or ltural commodity; (b)
the physiological condition ofthe plant or agricultural commodity; (c) the tration of
ens affecting the plant or agricultural commodity; (d) the type of disease injury on the
plant or ltural commodity; (e) weather conditions (e.g. temperature, humidity); and (f)
the stage of plant disease. According to the invention, typical concentrations are those higher
than 1 X 102 CFU/mL of carrier. Preferred concentrations range from about 1 X 104 to
about 1 X 109 CFU/mL, such as the trations ranging from 1 X 106 to 1 X 108
CFU/mL. More red concentrations are those of from about 35 to about 150 mg dry
WO 16361
microbial mass per gram of carrier (dry formulation) or per milliliter of carrier (liquid
composition). In solid formulations, the rate of application should be controlled to result in a
comparable number of viable cells per unit area of plant tissue surface as obtained by the
aforementioned rates of liquid treatment. Typically, the ical control agents of the
present invention are biologically effective when delivered at a tration in excess of 106
CFU/g (colony forming units per gram), preferably in excess of 107 CFU/g, more preferably
108 CFU/g, and most preferably at 109 CFU/g.
In some embodiments, the amount of one or more ofthe ical l agents
' in the microbial compositions ofthe present invention can vary depending on the final
formulation as well as size or type of the plant or seed utilized. Preferably, the one or more
biological control agents in the microbial compositions are present in about 2% W/w/ to about
80% w/w ofthe entire formulation. More preferable, the one or more biological control
agents employed in the compositions is about 5% W/W to about 65% w/w and most preferably
about 10% w/w to about 60% w/w by weight ofthe entire formulation.
As it will be appreciated by those skilled in the art, the microbiological
compositions of the invention may be applied to the Wheat plant or other cereals using a
variety of conventional methods such as dusting, coating, injecting, g, rolling, dipping,
spraying, or ng, or any other riate technique which does not significantly injure
the wheat plant or other cereals to be treated. Particularly preferred is the spray method.
Typically, the compositions ofthe invention are chemically inert; hence they are
ible with substantially any other constituents of the spray schedule. They may also be
used in combination with biologically compatible pesticidal active agents as for example,
ides, nematicides, fungicides, insecticides, and the like. They can also be used in
combination with plant grth affecting substances, such as fertilizers, plant growth
regulators, and the like, provided that such compounds or substances are biologically
compatible.
When used as pesticides or fungicide in their commercially available formulations
and in the use forms, prepared from these formulations, the active microbial antagonists and
compositions according to the present invention can furthermore be present in the form of a
mixture with synergists. Synergists are compounds by which the activity of the active
compositions is increased without it being necessary for the synergist added to be active
When used as pesticides in their commercially available formulations and in the
use forms, prepared from these formulations, the active microbial nists and
compositions according to the invention can furthermore be present in the form of a mixture
with inhibitors which reduce the degradation of the active compositions after application in
the habitat of the plant, on the surface of parts of plants or in plant tissues.
The active microbial antagonists and compositions according to the invention, as
such or in their formulations, can also be used as a mixture with known acaricides,
bactericides, fungicides, icides, microbicides, nematicides, pesticides, or combinations
thereof, for e in order to Widen the spectrum of action or to t the development
of resistances in this way. In many cases, synergistic effects result, 2'. e. the activity of the
mixture can exceed the activity of the individual components. A mixture with other known
active compounds, such as fertilizers, growth regulators, safeners and/or semiochemicals is
also contemplated.
In a preferred embodiment ofthe present invention, the compositions may further
include at least one chemical or biological pesticide. The amount of at least one chemical or
biological pesticide employed in the compositions can vary ing on the final
formulation as well as the size of the plant and seed to be treated. Preferably, the at least one
chemical or biological pesticide employed is about 0.1% w/w to about 80% w/w based on the
entire formulation. More preferably, the at least one chemical or biological pesticide is
present in an amount of about 1% w/w to about 60% w/w and most preferably about 10%
w/w to about 50% w/w.
A variety of ides is apparent to one of skill in the art and may be used.
Exemplary chemical ides include those in the carbamate, organophosphate,
organochlorine, and prethroid classes. Also included are chemical control agents such as, but
not limited to, benomyl, borax, captafol, , chorothalonil, ations containing
copper; formulations ning dichlone, an, iodine, zinc; fungicides that inhibit
ergosterol biosynthesis such as but not limited to blastididin, cymoxanil, fenarimol,
flusilazole, folpet,, imazalil, ipordione, maneb, manocozeb, metalaxyl,oxycarboxin,
utanil, oxytetracycline, PCNB, pentachlorophenol, prochloraz, propiconazole,
quinomethionate, sodium aresenite, sodium DNOC, sodium hypochlorite, sodium
phenylphenate, streptomycin, sulfur, tebuconazole, terbutrazole, thiabendazolel, thiophanate—
methyl, triadimefon, tricyclazole, triforine, validimycin, zolin, zineb, and ziram. A
variety of insecticidal compounds can be useful for the compositions ofthe invention,
including but not limited to those cited in U.S. Pat. Appl. No. 201 32A1.
The microbiological compositions ofthe present ion preferably include at
least one biological pesticide. Exemplary biological pesticides that are suitable for use herein
and can be included in a microbiological composition according to the present ion for
preventing a plant pathogenic disease include microbes, animals, ia, fungi, genetic
material, plant, and natural products of living organisms. In these compositions, the
microorganism ofthe present invention is isolated prior to formulation with an additional
organism. For example, microbes such as but not limited to species ofAmpelomyces,
Aureobasidium, Bacillus, Beauverz'a, Candida, Chaetomium, Cordyceps, Cryptococcus,
Dabaryomyces, Erwim'a, Exophilia, Gliocladium, Mariannaea, Paecilomyces, Paem'bacz'llus,
Pantoea, Pichia, Pseudomonas, olomyces, myces, and derma can be
provided in a composition with the nistic microorganisms of the present invention,
with fungal strains of the Muscodor genus being particularly red. Use of the
microbiological compositions according to the present invention in combination with the
microbial nists disclosed in US Patent No. 7,518,040; US Patent No. 7,601,346; US
Patent No. 6,312,940 is also particularly preferred.
Examples of fungi that can be combined with microbial antagonists and
compositions ofthe present invention in a ition include, without limitation, or
species, Aschersonia aleyrodz's, Beauverz'a bassiana ("white ine"), Beauveria
brongniartii, Chladosporium herbarum, Cordyceps clavulata, Cordyceps entomorrhiza,
Cordycepsfacis, Cordyceps gracilz's, Cordyceps melolanthae, Cordyceps militaris,
Cordyceps myrmecophz'la, Cordyceps ravenelz'i, Cordyceps sinensis, Cordyceps
cephala, Cordyceps subsessz'lis, Cordyceps unilateralz's, Cordyceps variabilis,
Cordyceps washingtonensis, Culicinomyces clavosporus, Entomophaga g‘ryllz', Entomophaga
maimaiga, Entomophaga muscae, Entomophagapraxibulli, phthoraplutellae,
Fusarz'um laterz'tium, Hirsutella citriformz's, Hirsutella thompsom', izium anisopliae
("green ine"), Metarhizz'umflaviride, Muscodor albus, Neozygitesfloridana, Nomuraea
rileyz', Paecilomycesfarinosus, Paecz'lomycesfumosoroseus, Pandora z'dz's,
Tolypocladz'um cylindrosporum, Verticillz'um lecam'z', Zoophthora radicans, and mycorrhizal
species such as Laccarz'a r. Other mycopesticidal species will be apparent to those
skilled in the art.
The present invention also provides methods of treating a plant by application of
any of a y of customary formulations in an effective amount to either the soil (1'. e. , in-
furrow), a portion of the plant (1'. e. , drench) or on the seed before planting (i.e., seed coating
or dressing). Customary formulations include solutions, emulsifiable concentrate, wettable
powders, suspension concentrate, soluble powders, granules, sion-emulsion
trate, natural and synthetic materials impregnated with active compound, and very fine
control release capsules in ric substances. In certain embodiments of the present
invention, the biological control compositions are formulated'in powders that are available in
either a ready-to-use formulation or are mixed together at the time of use. In either
embodiment, the powder may be admixed with the soil prior to or at the time of planting. In
an ative ment, one or both of either the biological control agent or insect control
agent is a liquid formulation that is mixed together at the time of treating. One of ordinary
skill in the art understands that an effective amount of the ive compositions depends on
the final formulation of the composition as well as the size of the plant or the size of the seed
to be treated.
Depending on the final formulation and method of application, one or more
suitable additives can also be introduced to the compositions of the t invention.
Adhesives such as carboxymethylcellulose and l and synthetic polymers in the form of
powders, es or latexes, such as gum arabic, chitin, polyvinyl alcohol and polyvinyl
acetate, as well as natural phospholipids, such as ins and lecithins, and synthetic
phospholipids, can be added to the present compositions.
In a preferred embodiment, the iological compositions are formulated in a
single, stable solution, or emulsion, or suspension. For solutions, the active chemical
compounds (i. e., the pest control agents) are typically dissolved in solvents before the
biological control agent is added. Suitable liquid solvents include eum based aromatics,
such as xylene, toluene or alkylnaphthalenes, aliphatic hydrocarbons, such as cyclohexane or
paraffins, f0r example petroleum fractions, mineral and vegetable oils, alcohols, such as
butanol or glycol as well as their ethers and esters, ketones, such as methyl ethyl ketone,
methyl isobutyl ketone or cyclohexanone, strongly polar solvents, such as
ylformamide and dimethyl sulphoxide. For emulsion or suspension, the liquid
medium is water. In one embodiment, the chemical control agent and biological control
agent are suspended in separate liquids and mixed at the time of ation. In a preferred
embodiment of suspension, the insect control agent and biologic are combined in a ready-to-
use formulation that exhibits a shelf-life of at least two years. In use, the liquid can be
sprayed or can be applied foliarly as an atomized spray or row at the time of planting
the crop. The liquid composition can be introduced to the soil before germination of the seed
or directly to the soil in contact with the roots by utilizing a y of techniques known in
the art including, but not limited to, drip irrigation, sprinklers, soil injection or soil drenching.
Optionally, stabilizers and buffers can be added, including alkaline and alkaline
earth metal salts and organic acids, such as citric acid and ascorbic acid, inorganic acids, such
as hydrochloric acid or sulfuric acid. Biocides can also be added and can include
formaldehydes or formaldehyde- releasing agents and derivatives of c acid, such as xybenzoic
acid.
Seed coating formulations
In some particularly preferred embodiments, the biocontrol compositions of the
present invention are formulated as a seed treatment. The seed treatment preferably
comprises at least one insect control agent and at least one biological control agent. It is
plated that the seeds can be substantially mly coated with one or more layers of
the trol compositions sed herein using conventional methods of mixing, spraying
or a combination thereof through the use of treatment application equipment that is
specifically designed and ctured to accurately, safely, and efficiently apply seed
ent products to seeds. Such equipment uses various types of coating technology such
as rotary s, drum coaters, fluidized bed techniques, spouted beds, rotary mists or a
combination thereof. Liquid seed treatments such as those of the present invention can be
applied Via either a spinning "atomizer" disk or a spray nozzle which evenly distributes the
seed treatment onto the seed as it moves though the spray pattern. Preferably, the seed is then
mixed or tumbled for an additional period oftime to achieve additional treatment distribution
and . The seeds can be primed or unprimed before coating with the inventive
compositions to increase the uniformity of germination and nce. In an alternative
embodiment, a dry powder formulation can be metered onto the moving seed and allowed to
mix until completely distributed.
Another aspect ofthe invention provides seeds treated with the subject
microbiological compositions. One embodiment provides seeds having at least part ofthe
surface area coated with a microbiological composition ing to the present invention. In
a specific embodiment, the microorganism-treated seeds have a spore concentration or
microbial cell concentration from about 106 to about 109 per seed. The seeds may also have
more spores or microbial cells per seed, such as, for example 1010, 1011 or 1012 spores per
seed. The microbial spores and/or cells can be coated freely onto the seeds or, preferably,
they can be formulated in a liquid or solid composition before being coated onto the seeds.
For example, a solid composition comprising the microorganisms can be ed by mixing
a solid carrier with a suspension of the spores until the solid carriers are impregnated with the
spore or cell suspension. This mixture can then be dried to obtain the desired particles.
In some other embodiments, it is contemplated that the solid or liquid biocontrol
compositions of the present invention further contain functional agents e of protecting
seeds from the harmful effects of selective herbicides such as activated carbon, nutrients
(fertilizers), and other agents capable of improving the germination and quality of the
products or a combination thereof.
Seed coating methods and compositions that are known in the art can be
particularly useful when they are d by the addition of one of the embodiments ofthe
present invention. Such g methods and apparatus for their application are disclosed in,
for e, U.S. Pat. Nos. 5,918,413; 5,554,445; 5,389,399; 945; and 4,465,017.
Various seed coating itions are disclosed, for example, in U.S. Pat. Appl. Nos.
US20110033432, US20100154299, U.S. Pat. Nos. 5,939,356; 5,876,739, 5,849,320;
084, 5,661,103; 544, 5,328,942; 4,735,015; 4,634,587; 4,372,080, 4,339,456; and
4,245,432, among others. '
A variety of additives can be added to the seed treatment formulations comprising
the inventive itions. Binders can be added and include those composed preferably of
2012/048012
an ve polymer that can be natural or synthetic without phytotoxic effect on the seed to
be coated. The binder may be selected from polyvinyl acetates; polyvinyl acetate
copolymers; ethylene vinyl e (EVA) copolymers; polyvinyl alcohols; polyvinyl alcohol
mers; celluloses, including ethylcelluloses, methylcelluloses,
hydroxymethylcelluloses, hydroxypropylcelluloses and carboxymethylcellulose;
polyvinylpyrolidones; polysaccharides, including , modified starch, dextrins,
maltodextrins, alginate and chitosans; fats; oils; proteins, ing gelatin and zeins; gum
arabics; shellacs; Vinylidene chloride and dene chloride copolymers; calcium
lignosulfonates; c copolymers; nylacrylates; polyethylene oxide; acrylamide
polymers and copolymers; polyhydroxyethyl acrylate, methylacrylamide monomers; and
polychloroprene.
Any of a variety of colorants may be employed, including organic chromophores
classified as nitroso; nitro; azo, including monoazo, bisazo and polyazo; acridine,
anthraquinone, azine, diphenyhnethane, indamine, indophenol, e, e,
ocyanine, thiazine, thiazole, triarylmethane, xanthene. Other additives that can be
added include trace nutrients such as salts of iron, manganese, boron, copper, cobalt,
molybdenum and zinc. A polymer or other dust control agent can be applied to retain the
treatment on the seed surface.
In some specific embodiments, in addition to the microbial cells or spores, the
coating can fiirther comprise a layer of adherent. The adherent should be non-toxic,
biodegradable, and adhesive. Examples of such materials include, but are not limited to,
polyvinyl acetates; polyvinyl acetate copolymers; polyvinyl alcohols; polyvinyl alcohol
copolymers; celluloses, such as methyl celluloses, hydroxymethyl celluloses, and
hydroxymethyl propyl oses; dextrins; alginates; sugars; molasses; polyvinyl
pyrrolidones; polysaccharides; proteins; fats; oils; gum arabics; gelatins; syrups; and starches.
More examples can be found in, for e, US. Pat. No. 7,213,367 and US. Pat. Appln.
No. US20100189693.
Various additives, such as adherents, dispersants, surfactants, and nutrient and
buffer ients, can also be included in the seed treatment formulation. Other
conventional seed treatment additives include, but are not limited to, coating agents, wetting
, buffering agents, and polysaccharides. At least one agriculturally acceptable carrier
can be added to the seed treatment formulation such as water, solids or dry powders. The dry
powders can be derived from a variety ofmaterials such as calcium carbonate, gypsum,
vermiculite, talc, humus, activated charcoal, and various phosphorous compounds.
In some embodiment, the seed coating composition can comprise at least one filler
which is an organic or inorganic, natural or synthetic component with which the active
components are combined to facilitate its application onto the seed. Preferably, the filler is
an inert solid such as clays, natural or synthetic silicates, silica, resins, waxes, solid fertilizers
(for example ammonium salts), natural soil minerals, such as s, clays, talc, lime, quartz,
attapulgite, montmorillonite, ite or diatomaceous , or synthetic minerals, such as
silica, alumina or silicates, in particular um or magnesium silicates.
The seed treatment formulation may further include one or more ofthe following
ingredients: other pesticides, including nds that act only below the ground;
fimgicides, such as captan, thiram, metalaxyl, fludioxonil, oxadixyl, and isomers of each of
those materials, and the like; herbicides, including compounds selected from sate,
carbamates, rbamates, acetamides, triazines, dinitroanilines, glycerol ethers,
zinones, s, phenoxys, ureas, and c acids; herbicidal safeners such as
benzoxazine, benzhydryl derivatives, N,N—diallyl dichloroacetamide, various dihaloacyl,
oxazolidinyl and thiazolidinyl compounds, ethanone, naphthalic anhydride compounds, and
oxime derivatives; fertilizers; and biocontrol agents such as other naturally-occmring or
recombinant bacteria and fungi from the genera Rhizobium, Bacillus, Pseudomonas, Serratia,
Trichoderma, Glomus, Gliocladium and hizal fungi. These ingredients may be added
as a separate layer on the seed or alternatively may be added as part of the seed coating
composition ofthe invention.
Preferably, the amount of the novel composition or other ients used in the
seed ent should not inhibit ation of the seed, or cause phytotoxic damage to the
seed.
The microorganism-treated seeds may also be further enveloped with a film
overcoating to protect the coating. Such overcoatings are known in the art and may be
applied using fluidized bed and drum film coating techniques.
WO 16361
In principle, any plant seed capable of germinating to form a plant that is
susceptible to attack by nematodes and/or pathogenic fungi can be treated in accordance with
the invention. Suitable seeds include those of cereals, coffee, cole crops, fiber crops, flowers,
fruits, legume, oil crops, trees, tuber crops, vegetables, as well as other plants of the
monocotyledonous, and dicotyledonous species. Preferably, crop seeds are coated which
include but are not limited to bean, , corn, cotton, grasses, lettuce, peanut, pepper,
potato, rapeseed, rice, rye, sorghum, soybean, sugar beet, sunflower, tobacco, and tomato
seeds. Most preferably, barley or wheat (spring wheat or winter wheat) seeds are coated with
the t compositions.
Also ed, in another aspect of the present invention, is a novel cereal plant
created by artificially introducing a ial endophyte ofthe invention into a cereal plant
that is free of endophytic microorganisms. In some ments ofthis aspect, the microbial
endophyte introduced into the cereal plant may be an endophytic antagonist having
suppressive activity against head blight disease or a causative agent of head blight disease.
Furthermore, the endophytic antagonist introduced into the cereal plant may be the fungal
strain SGI—OlO-Hl l. A variety ofmethods previously found effective for the introduction of
a microbial endophyte into cereal grass species are known in the art. Examples of such
methods include those described in US. Pat. Appl. No. 20030195117A1, US. Pat. Appl. No.
20010032343Al, and US Pat. No. 7,084,331, among others. It will become apparent to
those skilled in the art that many of the aforementioned methods can be useful for the making
of a novel cereal plant of the invention.
After ial infection, it is preferred that DNA ofthe ed endophytic
antagonist is ied by PCR and the antagonist is ed by ng out a homology
search for the DNA amplified. Further it is preferred that a foreign gene that expresses an
identifiable means is introduced into the above-mentioned endophytic antagonist, and the
presence of the colonization of the above—mentioned endophytic antagonist infecting the plant
is ed by the above-identifiable means using the foreign gene.
Preparing the trol compositions according to the present invention
Cultures ofthe ial antagonists may be prepared for use in the biocontrol
compositions ofthe invention using standard static drying and liquid fermentation techniques
known in the art. Growth is commonly effected in a bioreactor.
A bioreactor refers to any device or system that supports a biologically active
environment. As described herein a bioreactor is a vessel in which microorganisms including
the ial antagonists of the invention can be grown. A bioreactor may be any
appropriate shape or size for growing the microorganisms. A bioreactor may range in size
and scale from 10 mL to liter’s to cubic meters and may be made of stainless steel or any
other appropriate material as known and used in the art. The bioreactor may be a batch type
bioreactor, a fed batch type or a continuous-type bioreactor (e.g. , a continuous stirred
reactor). For example, a bioreactor may be a chemostat as known and used in the art of
iology for growing and ting bacteria. A bioreactor may be obtained from any
commercial supplier (See also Bioreactor System Design, Asenjo & Merchuk, CRC Press,
1995).
For small scale operations, a batch bioreactor may be used, for example, to test and
develop new processes, and for processes that cannot be converted to continuous operations.
Microorganisms grown in a ctor may be suspended or immobilized. Growth
in the bioreactor is generally under aerobic conditions at suitable temperatures and pH for
growth. For the organisms of the invention, cell growth can be ed at temperatures
n 5 and 37°C, with the preferred temperature being in the range of 15 to 30°C, 15 to
28°C, 20 to 30°C, or 15 to 25°C. The pH ofthe nutrient medium can vary between 4.0 and
9.0, but the preferred operating range is usually slightly acidic to neutral at pH 4.0 to 7.0, or
4.5 to 6.5, or pH 5.0 to 6.0. Typically, maximal cell yield is obtained in 20-72 hours after
inoculation.
Optimal conditions for the cultivation of antagonists of this invention will, of
in the
course, depend upon the particular strain. However, by virtue of the ions d
selection s and general requirements of most microorganisms, a person of ordinary
skill in the art would be able to determine essential nutrients and conditions. The microbial
nists would typically be grown in aerobic liquid cultures on media which contain
sources of carbon, nitrogen, and inorganic salts that can be lated by the microorganism
and supportive of efficient cell growth. Preferred carbon sources are hexoses such as
glucose, but other sources that are readily assimilated such as amino acids, may be
substituted. Many nic and proteinaceous materials may be used as nitrogen sources in
the growth process. Preferred nitrogen sources are amino acids and urea but others include
gaseous ammonia, nic salts of nitrate and ammonium, vitamins, purines, dines,
yeast extract, beef extract, proteose peptone, soybean meal, hydrolysates of casein, distiller's
solubles, and the like. Among the inorganic minerals that can be incorporated into the
nutrient medium are the customary salts capable of yielding calcium, zinc, iron, manganese,
magnesium, , cobalt, potassium, sodium, molybdate, phosphate, sulfate, chloride,
borate, and like ions. Without being limited thereto, use of potato dextrose liquid medium for
fungal antagonists and R2A broth premix for ial strains is preferred.
Throughout this disclosure, various information sources are referred 'to and
incorporated by reference. The information sources include, for example, scientific journal
articles, patent documents, textbooks, and World Wide Web r—inactive page addresses.
The reference to such ation sources is solely for the purpose ofproviding an indication
of the general state of the art at the time of filing. While the ts and teachings of each
and every one ofthe information s can be relied on and used by one of skill in the art to
make and use embodiments of the invention, any discussion and comment in a specific
information source should in no way be considered as an admission that such comment was
widely accepted as the general opinion in the field.
The discussion of the general methods given herein is intended for illustrative
purposes only. Other ative methods and embodiments will be apparent to those of skill
in the art upon review of this disclosure, and are to be included within the spirit and purview
ofthis application.
It should also be understood that the following examples are offered to rate,
but not limit, the invention.
EXAMPLES
EXAMPLE 1: Discoveg of the antagonistic microorganisms capable of suppressing the
development ofFusarz'um gramz'naerum and Gibberella zeae, causative agents of head blight
disease.
This example describes a high-throughput process of collecting and screening
candidate microorganisms that has been developed internally at Synthetic Genomics, Inc. to
isolate strains of microorganisms having suppressive activity against causative agents ofhead
blight disease, particularly against Fusarium graminearum. Novel ial nistic
strains were isolated from plant tissue samples collected from several locations across the
United States. The bacterial strains SGIC06, SGI—Ol4-G01, SGI-OlS-F03, and SGI—
015-H06 were isolated from plant root tissues collected from Eagle Peak Preserve near
, CA. The fungal strain SGI-OlO-Hll and the ial strain SGI-OOS-GOS were
isolated from stem tissues oftwo different plant samples collected from San Elijo Lagoon,
Encinitas, CA.
The rganisms were isolated as follows. For bacterial strain ion, plant
root tissues were sonicated and subjected to serial dilutions on 2><YT (yeast extract and
tryptone) and N—free agar medium plates. Individual colonies were then selected based on
morphological characteristics, and dually cultured in liquid broth medium. For fimgal
isolation, plant tissue was first surface-sterilized by dipping in 70% l and briefly
passing through a flame. The tissue was then dissected and placed on potato dextrose agar
(PDA) medium, followed by incubation at room temperature. When mycelial growth was
observed, a segment of mycelial growth was then transferred to another PDA plate. Strains
of microorganisms were isolated, d and preserved at —80°C in 15% glycerol at for
bacterial strains and on dried barley seed for fungal strains.
Strains ofmicroorganisms ed as described above were thereafter assayed for
their ability to suppress mycelial growth ofE graminearum in an in vitro antagonism test,
which was performed on agar plates containing potato dextrose agar (PDA) growth medium
according to a high-throughput screening procedure described in US. Pat. Appl. No.
U820120107915A1, which is incorporated by reference , with minor ations.
Briefly, isolated strains oorganisms were grown on one-fifth strength Tryptic soy
broth agar S) for 24 hours prior to use. Conidial inoculum of F. gmmz'nearum
NRRL—S883 was ed by hyphal tipping an actively growing colony ofthe fungus and
transferring the hyphal strands to PDA agar medium. After incubating the plates for 7 days at
°C using a 12 h/day photoperiod, conidia were washed from PDA plates using a weak
phosphate buffer % phosphate buffer, pH 7.2, with 0.019% MgClz). A suspension of
conidia of F. graminearum in the weak phosphate buffer (1 X 105 conidia/m1) was then
immediately spread over the agar surface, and the plates were then incubated at 25°C for 48-
72 hours. To initiate the antagonism test, cells of isolated microbial s were point-
inoculated at equal distances inside the perimeter of the plate. After five days, the s
were scored as antibiosis positive when a y clear area that lacked mycelial growth
existed around the perimeter of the microbial colonies.
More than 4,000 microbial strains were isolated and assayed by the procedure
bed above. e, six strains were found to significantly suppress the mycelial
growth ofF. gramz‘nearum NRRL—5883 on PDA medium. These new microbial antagonists
are fied as SGI—005-G08, SGI-OlO-Hl 1, 4-CO6, SGI—014-G01, SGI-OlS-F03,
and SGI-Ol 5—H06.
Antagonism test was also performed for the new microbial antagonists for their
ability to suppress the growth of fungal pathogen Gibberella zeae, which is a teleomorphic
species ofFusarz'um graminearum. All procedures were identical to those described above,
except that the pathogen strain tested in this assay was a pathogenic strain of the fungus
Gibberella zeae. Of these six microbial antagonists, four strains O-Hl 1, SGI—014-
C06, SGI—015-F03, and SGI—015-H06 were found to significantly suppress the mycelial
growth of Gibberella zeae.
EXAMPLE 2: DNA extraction, Sequencing and Taxonomy
Fungal Cell Lysis and Acquiring ITS-5.88 rDNA Sequence Information
The fungal biomass was transferred to a 96—well PCR microplate containing 50 ul
of a 2 X lysis buffer (100 mM Tris HCL, pH 8.0, 2 mM EDTA, pH 8.0, 1% SDS, 400 ug/ml
Proteinase K). Lysis conditions were as follows: 55°C for 60 minutes, 94°C for 4 minutes.
An aliquot ofthe lysis product was used as the source oftemplate DNA for PCR
amplification. The ITS-5.88 rDNA sequence was amplified via PCR using two primers
SI (SEQ ID NO: 15) and ITS4 iled (SEQ ID NO: 16).
For amplification ofthe ITS-5.88 rDNA region, each PCR mixture was prepared in
a 20-ul final volume reaction containing 4 ul from the flmgal lysis reaction, 0.2 uM of each
primer (ITSl/ITS4), 6% Tween-20, and 10 ul of 2X ImmoMix (Bioline USA Inc, Taunton,
MA). PCR ions were as follows: 94°C for 10 minutes; 94°C for 30 seconds, 52°C for
seconds, 72°C for 75 seconds for 30 cycles; 72°C for 10 minutes. A 2-ul aliquot ofthe
PCR product was run on a 1.0% agarose gel to confirm a single band ofthe expected size.
Positive bands were sent out-for Sanger sequencing in the d and reverse directions
using M13 primers. Sequence of the 5.88 enic region (ITS) of the fungal strain SGI-
l is provided in the Sequence Listing as SEQ ID NO: 11. Homology search for the
determined nucleotide sequence ofthe 5.88 intergenic region (ITS) was conducted using the
DDBJ/GenBank/EMBL database. Subsequently, the phylogenetic relationship of the
nucleotide sequence of the 5.88 enic region (ITS) was analyzed among the isolated
fungal antagonist SGI-OlO—Hll described herein, rganisms of the genera and species
that t high sequence homologies to the isolated fungal antagonist SGI-OlO-Hl 1, and
other wide ies of rganism genera and, species, using the ClustalW phylogenetic
tree ng program. The fimgal strain SGI-OlO-Hll is considered to be related to the
family of Mycosphaerellaceae based upon ~97% similarity of its ITS-5.88 rDNA sequence to
those ofMycosphaerella punctiformz‘s (GenBank EU343182) and Ramularz'a pratensz's
(GenBank EU019284), whose 5.8S ITS sequences show clear relatedness to
Mycosphaerellaceae.
Bacterial Cell Lysis and Acquiring 16S rRNA Sequence Information
A 20-ul aliquot of cell suspension was transferred to a 96-well PCR plate
containing 20 pl of a 2)< lysis buffer (100 mM Tris HCL, pH 8.0, 2 mM EDTA, pH 8.0, 1%
SDS, 400 ug/ml Proteinase K). Lysis conditions were as follows: 55°C for 30 minutes, 94°C
for 4 minutes. An aliquot of the lysis product was used as the source of template DNA for
PCR amplification. The 16S rRNA sequence was amplified via PCR using M13—27F (SEQ
ID NO: 17) and 1492R M13-tailed (SEQ ID NO: 18) primers.
For amplification of 16S rRNA region, each PCR mixture was prepared in a 20—u1
final volume reaction containing 4 pl from the bacterial lysis reaction, 2 uM of each primer
(27F/1492R), 6% Tween-20, and 10 ul of 2X ImmoMix (Bioline USA Inc, Taunton, MA).
PCR conditions were as s: 94°C for 10 minutes; 94°C for 30 seconds, 52°C for 30
seconds, 72°C for 75 seconds for 30 cycles; 72°C for 10 s. A 2-ul aliquot ofthe PCR
product was run on a 1.0% agarose gel to confirm a single band ofthe expected size. Positive
bands were sent out for Sanger sequencing in the forward and e directions using M13
primers. Sequences of the 16S rRNA ofthe bacterial strains SGIC06, SGI-OOS-GOS,
SGI—014-G01, SGIF03, and SGI—OlS—H06 are approximately 1.4—Kb in length and are
provided in the Sequence Listing as SEQ ID NOS: 1, 10, 12, 13, and 14 respectively.
Homology search for the determined nucleotide ce was conducted using the
DDBJ/GenBank/EMBL database. Subsequently, the phylogenetic relationship of the
tide sequence ofthe 16 rRNA genes was analyzed among the isolated bacterial
antagonists described , bacteria of the genera and species that exhibit high sequence
homologies to the isolated bacterial antagonists, and other wide ies of bacterial genera
and species, using the ClustaIW phylogenetic tree building program. Sequence identity and
rity were also determined using GenomeQuestTM software (Gene-1T, Worcester Mass.
USA). The sequence is result revealed that the bacterial isolate SGI—014—G01 can be
considered to be related to the genus of Variovorax based upon ~99% rity of its 16S
rRNA sequence to those of several Variovorax species, including Variovorax sp. R—21938
(GenBank AJ786799) and Variovoraxparadoxus (GenBank GU186109), whose 16S rRNA
sequences show clear dness to Variovorax sp. Further, the sequence analysis result also
revealed that the two bacterial isolates SGI-015—F03 and SGI—015-H06 can be considered to
be related to the family ofBacillaceae, based upon >99% similarity of their tive 168
sequences to those of several Bacillus spp.
The sequence analysis result revealed that the two bacterial isolates SGI—014-C06
and SGIG08 can be considered to be related to the family of Microbacteriaceae based
upon >99% similarity of their respective l6S sequences to those of several acz‘erz’um
spp. Notably, the 1430-nt sequence ofthe 16S rRNA gene of SGIC06 (SEQ ID NO: 1)
is identical to the 16S rRNA gene of a Microbacterium oxydcms strain DSM 20578 and
several other Mcrobacterium sp. strains (e.g.
, k sequences Y17227.1, FJ200406,
EU086800, and EU714335) over its entire 1430-nt length.
WO 16361
In particular, among the thousands ofmicrobial strains that were isolated and
tested for the ability to suppress Fusarium development in antagonism
assays as described in
Example 1, a total of —eight strains was subsequently identified as Microbacterz'um
species based upon the sequence similarity of their 168 sequences to those n
Microbacterium spp. However, Applicants have found that SGI—014-C06 and SGI—OSS-GOS
were the only two Microbacterium strains that possessed suppressive activity against
Fusarium graminearum. To date, as discussed above, several naturally occurring microbes
have been reported as having antagonistic activity against head blight disease. However,
there are no reports prior to the present invention that describe a microorganism of the
genus
cterium having such antagonistic ty. Further, prior to the present invention, the
present inventors were not aware of any methods or processes of using a bacterial strain of
the genus cterz'um as biocontrol agent in preventing, inhibiting or treating the
development of a causative en ofhead blight e.
EXAMPLE 3: Sequence Analysis of Housekeeping Genes from the Isolate SGI—Ol4-C06
A phylogenetic study of several housekeeping genes from 27 species of the
genus
Microbacterz'um has been reported recently by Richert et al. (Syst. App]. Mcrobiol. 30: 102-
108, 2007). The study concluded that although the merits of the 16S rRNA sequence analysis
for systematic taxonomy are unsurpassed, sole emphasis on a single mic parameter
' should
not guide systematic conclusions. As disclosed above, the nucleotide sequence ofthe
16S rRNA gene of SGIC06 (SEQ ID NO: 1) is identical to the 16S rRNA
gene of
several Microbacterium sp. strains, including the nucleotide sequence of a 16S rRNA
gene of
a acterium oxydans strain DSM 20578 that was included in t et al. (2007) study
(GenBank Accession Y17227.1). Applicants proceeded to m a phylogenetic analysis
on four housekeeping genes ofthe isolate SGIC06, which are DNA gyrase subunit B
(gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA), and polyphosphate kinase
(ppk). Toward this end, the entire genome of the isolate SGI-014—C06 was shot—gun
sequenced, assembled and ted by using procedures described in PCT Patent
Application No. W02010115156A2. Genomic DNA was ed from a fresh culture of
SGIC06. Cell pellet was used for high molecular weight DNA extraction using the
U1traC1ean® Mega Soil DNA Isolation Kit (Cat. No 12900-10) from MO BIO Laboratories,
Inc. according to the manufacture’s recommended protocol. The genomic DNA from SGI—
014-C06 was then prepared for shotgun 454-pyrosequencing. Genomic DNA (7.5ug) was
used for library construction according to the ended protocol (454 Life Sciences) for
single long reads. The sequences were generated by two GS FLX Titanium series sequencing
111113.
The sequences of four housekeeping genes gyrB, rpoB, recA, andppk ofthe isolate
SGIC06 are provided in the Sequence Listing. Homology search for the determined
nucleotide sequences was conducted using the DDBJ/GenBank/EMBL database. Sequence
identity and similarity were also determined using GenomeQuestTM software (Gene-IT,
Worcester Mass. USA). As discussed in details below, the result of sequence analysis ofthe
housekeeping genes revealed that the isolate SGIC06 described in the t disclosure
is a novel bacterial strain and can be considered to be related to the family of
Microbacteriaceae.
The polynucleotide sequence ofthe gyrB gene of SGI-Ol4-C06 has the st
sequence identity with a gyrB gene obacterium testaceum having GenBank accession
number AP012052 (82.69% over a 936/2172 nucleotide alignment). When compared to the
gyrB gene ofthe Microbacterium s strain DSM 20578 (GenBank AM181493; Richert
et al., 2007), the sequence gies between the two genes were ~62% identical at the
tide level and ~37% identical at the amino acid level.
The polynucleotide sequence of the rpoB gene of SGI—Ol4-CO6 has the greatest
sequence identity with an rpoB gene ofMicrobacterium maritypz‘cum having GeneBank
accession number AM181582 (96.98% over a 1093/3504 nucleotide alignment). When
ed to the rpoB gene of the Microbacz‘erium s strain DSM 20578 (GenBank
83; Richert et al., 2007), the sequence homologies between the two genes were
~96% identical at the tide level and 99% identical at the amino acid level.
The polynucleotide sequence of the recA gene of 4—C06 has the greatest
sequence identity with a recA gene ofMicrobacterium testaceum having GeneBank accession
number AP012052 (85.45% over a 962/1188 nucleotide alignment). When compared to the
recA gene ofthe Microbacterium oxydans strain DSM 20578 (GenBank AM181527; Richert
et al., 2007), the sequence homologies between the two genes were ~92% identical at the
nucleotide level and 100% identical at the amino acid level.
The polynucleotide sequence of theppk gene of SGI—Ol4-C06 has the greatest
sequence identity with appk gene ofMicrobacterium luteolum having k accession
number AM181554 (91.38% over a 1380/2175 nucleotide alignment). When compared to
the ppk gene ofthe Microbacterium oxydans strain DSM 20578 (GenBank AM181556;
Richert et al., 2007), the sequence homologies between the, two genes were ~91% identical at
the tide level and ~98% identical at the amino acid level.
EXAMPLE 4: tion of wheat from Fusarium graminearum infection using the microbial
antagonists Microbacterium Sp. [ERRL B-50470) Mycophaerella sp. (N BBL 50471 1, and
Variovorax sp. [EBB]: B-50469)
Microbial strains that were found positive for antibiosis in the antagonism screen
bed in Example 1 were further ted through a plant-based bioassay in which cells
of the microbial strains were applied directly onto seeds of a susceptible cereal ar,
followed by inoculation with al spores of F. grarninearum. The ial strains were
grown to a sufficient turbidity and diluted in water. Two gram ofwheat seeds of a
susceptible wheat cultivar (Hank; WestBred LLC, n, MT) were sown in one-liter pots
containing pasteurized soil medium. After sowing, 20 mL ofthe microbial culture dilution
was transferred on top of sown seeds. The wheat seeds were allowed to germinate in
greenhouse conditions under fluorescent lighting with a 14 hour photoperiod. At the onset of
wheat flowering, the wheat heads were nged by spraying with F. graminearum NRRL
5883 conidial spores. al spores were ted from five day old PDA plates by
pouring water with 0.01% Tween20 on plates and scraping spores into suspension. After
spraying spores, wheat plants were transferred to a mist chamber with 100% humidity for
three days to allow for infection. The treatments were:
l. Untreated: no microbial or chemical fungicide treatment + Fusarium challenge.
. 2. Non-infected: no microbial or chemical fungicide treatment, no ’um
challenge.
3. SGI—Ol O-Hl 1: fimgal treatment + Fusarium challenge.
4. SGI—014-G01: bacterial treatment + Fusarz'um challenge.
5. SGI-Ol4-C06: bacterial treatment + Fusarium challenge.
Twenty days after infection, watering was stopped and wheat plants were d
to dry for three weeks before harvesting. Individual wheat heads were ted and
collected. Disease severity was determined for each head showing head blight disease
symptoms. Disease severity was calculated as the number of diseased spikelets divided by
the total number of ets per heads. The results (TABLE 2) revealed that wheat plants
treated with each of the three microbial antagonists tested, SGI-014—C06 (NRRL B-50470),
SGI—OlO-Hll (NRRL 50471), and SGI—014-G01 (NRRL B-50469), had significantly lower
severity and nce rz'um graminearum infestation 'when compared to the
“untreated” control growing in the same conditions (P<0.05).
The seeds from each head were harvested by hand and the seed mass was weighed.
The average seed weight per pot in each ofthe treatments was calculated. As reported in
TABLE 3, each ofthe ial antagonists was found to significantly reduce yield loss
caused by head blight infestation.
TABLE 2. Efficacy ofthe microbial antagonists in reducing head blight incidence in Wheat.
Percent severity (%) STDEV
SGI—OlO—Hll 0.0219 0.0005
SGI—014-G01 0.0315 0.0001
SGI—014-C06 0.0225 0.0004
TABLE 3. Efficacy of the microbial antagonists in preserving seed yield in wheat plants
having head blight disease.
0.8438i0.1633 0.0191
SGI—OlO-Hll 0.6200 i 0 1844 0.7025
SGI—Ol4-G01 0.7963 3: 0 2032 0.5277
SGI—014-C06 7
0.6744 :i: 0.0948 0.0551
EXAMPLE 5: Growth tion ofFusarz'um graminearum by microbial antagonists on
Was.
The ial strains found to possess suppressive activity against F. graminearum
in antagonism plate assay were investigated further for their ability to reduce the incidence of
head blight in wheat. Seeds of a susceptible wheat cultivar (Hank; ed LLC, Bozeman,
MT) were sown in l-Liter pots each ning pasteurized soil medium in 20 cm diameter
plastic pots. Microbial cell suspensions were prepared as follows.2YT, or similar growth
medium, broth cultures were inoculated from isolate glycerol stocks or streak plates.
Typically, cultures were initiated 48 - 72 hours prior to use in the growth chamber,
greenhouse or field allowing the culture to reach late ntial phase. Isolates that have
longer doubling times were initiated further in advance. Cultures were incubated at 30°C on
a rotary shaker at 200 rpm. After growth, the cells were pelleted at 10,000 x g for 15 min at
4°C and re-suspended in 10 mM MgSO4 buffer (pH 7.0). Cell densities were normalized for
each isolate on a CFU/mL basis (cell performing units per milliliter). Typically, ~109 CFU/
mL suspensions were prepared for each isolate and transported to the ation site on ice.
Inoculations were performed by diluting these cell suspensions 1/20 in irrigation water to a
final density 5 X 107 CFU/mL. For 1-L pot , 20 mL of this dilute cell suspension was
buted evenly over the e of each replicate pot. For micro-trial pots, cell
suspensions were not diluted and 1 mL of each 109 CFU/mL sion was pipetted directly
onto the surface of each replicate pot as soil drench on top of the submerged seeds. The
seeds and plants were maintained in a greenhouse at room temperature with a 14 h
photoperiod of light.
Mycelium of the Fusarium gramz’nearum strain NRRL-5883 was grown on PDA
plates for 5 days under constant light. Hyphae and conidia were harvested by g a few
mL of e water (0.01% Tween 20) on the plates and scraping the agar surface with a
sterile spatula. The tration of spores in the inoculum was approximately 2><105
spores/mL, but hyphal fragment concentration was not determined.
Inoculation with F. graminearum began after shoot emerging from the seeds and
continued every other evening for 10 days. The inoculum of F. gramz'nearum was applied
with a sprayer at about 30 mL per pot. Immediately after each inoculation, the plants were
misted with overhead mister. When chemical fungicide was used, the fungicide (Banner
Maxx, Syngenta) was prepared by diluting 2 mL of fungicide stock in IL of distilled water,
and was applied with a sprayer at about 30 mL per pot.
Head blight was evaluated by the severity ofFusarium infestation, as determined
by the number ofFusarium colony-forming units per gram (CFU/g) ofplant tissues. All
treatments were performed in four blocks with four ate pots. The treatments were:
1. Untreated: no microbial or chemical fungicide treatment, + Fusarz'um challenge.
2. Non-infected: no microbial or chemical fungicide treatment, no Fusarium
challenge.
3. Fungicide: chemical fungicide treatment + Fusarium challenge.
4. SGI-OlO-Hl 1: fungal treatment + Fusarium challenge.
5. SGIG01: bacterial treatment + Fusarz’um challenge.
6. SGI-014—C06: bacterial treatment + Fusarium challenge.
The results, as ed in TABLE 4, revealed that all three microbial treatments
ed a significant decrease in FHB severity as compared to the infected control. In
particular, two microbial antagonists, 4-C06 and SGI—OlO-Hl 1, significantly reduced
the infestation of Wheat plants by um gramz’nearum when compared to the untreated
control grown in the same conditions. The tion of Wheat plants from 'um
infestation effected by each of the two microorganisms SGI—014-C06 and O-Hll was
statistically comparable to the protection effected by the commercial al fungicide.
When the microorganism SGIG01 was applied, the observed protection of wheat plants
from Fusarz'um infestation was much less conspicuous and its effectiveness varied greatly
among the replicate pots.
TABLE 4: Effect ofmicrobial antagonists on Fusarz'um ation.
Treatment CFU/g
Untreated 487 :l: 600
Non-infected <.0001
Chemical fungicide 290 i 146 <.0001
SGI-OlO—Hll 671 i 450 0.0077
4-G01 1246 i 465 0.8387
SGI—014-C06 367 i 234 0.0001
EXAMPLE 6: Growth and stora e of the microbial anta onists
Mycosphaerella sp.: Several methods were used to store the isolated fungus as a
pure culture, one of which was the filter paper technique. The fungus was also allowed to
grow on PDA, and then it was cut into small squares which were placed into vials containing
% glycerol and stored at —70°C. The fungus was also stored at 4°C by a similar method,
using distilled water rather than glycerol. However, one of the preferred methods of storage
was on infested sterile barley seed at -80°C.
Bacillus sp., Microbacterz'um Sp. and Variovorax sp.: The isolated bacteria were
stored as a pure culture. A bacterial colony was transferred to a vial containing R2A broth
liquid medium (Tecknova) and allowed to grow at 30°C with shaking at 250 rpm for two
days. The culture was then transferred into vials containing 15% glycerol and stored at —
80°C.
EXAMPLE 7: Spore tion and seed coating treatments
Spore tion: In a typical spore production procedure, one liter of2XYT
growth medium (16 g/L ne, 10 g/L yeast extract, 5 g/L NaCl) was ated with 5
mL starter e or petri dish scraping and incubated overnight at 30°C in a ng shaker
that was set at 225 rpm. Bacterial cells were pelleted by centrifugation, and washed 1x with
PBS buffer (8 g/L NaCl; 0.2 g/L KCI; 1.44 g/L NazHPO4; 0.24g of KH2P04; pH 7.4). Cells
were resuspended in CDSM medium (Hageman et al., J Bacteriol., 43 8-441, 1984), and
were grown for four additional nights at 30°C in the rotating shaker. Sporulation in the
bacterial culture was monitored daily by using phase contrast microscope until the entire
culture was virtually made up of free-floating spores. The tion time typically took less.
than four days or more than six days depending on the s. Under phase contrast
microscope, endospores were detected within cells as bright white oblate spheroids. Bacterial
spores were pelleted by centrifugation at 10,000 X g for 15 minutes, washed two times with
sterile dH20 and, if necessary, concentrated down to 50 mL and could either be used
immediately or refrigerated for later use. Spore concentration was measured at 0D600. This
procedure typically produced at least 2000 OD's of bacterial spores.
In particular, several bacterial strains of the present invention, e.g. Bacillus sp.
SGIF03, could conveniently produce large amounts of spores after 4 days of incubation
with a simple inoculation of a large overnight starter culture (~15 ml.) in to 1 liter of 2>< SG
growth medium, followed by a 4-day incubation at appropriate temperature in a rotating
shaker set at 225 rpm. The recipe of the 2x SG growth medium was as follows: 16 g/L
Nutrient Broth; 0.25 g/L MgSO4; 2.0 g/L KCl; 0.15 g/L 2H20; 0.025 g/L MnC12.2H20;
0.28 mg/L FeSO4-7H20; 1.0 g/L Dextrose.
Seed coating treatments ofwheat and corn seeds: Small-scale seed treatment
experiments were conducted by ing a procedure described in Sudisha et al. , 2009 with
minor ations. Typically, a biopolymer stock solution was made by adding 6 gram of
gum Arabic powder (MP Biomedical) to 36 mL water in a 50 mL Falcon tube, which was
subsequently mixed to neity by using a wheel mixer. A stir plate was used for
mixing when larger quantities of coated seeds were .
When vegetative cells were used, turbid cultures of actively growing microbial
cells were washed with PBS and adjusted to an OD600 of ~5.0. Alternatively, microbial spore
suspensions were prepared as described above. Bacterial spores and/or vegetative cells were
thoroughly resuspended in ~32 mL gum Arabic biopolymer stock solution prepared as
described above, and resulting suspension was mixed thoroughly in a 1 L bottle.
Approximately 400 g of seeds (either wheat or corn) were added to the bottle and vigorously
shaken or vortexed to ensure a m distribution ofthe ll sion. Coated seeds
were then spread across a sterile plastic weigh boats to dry in a laminar flow hood until no
longer tacky, generally 3-6 hours with periodic . In some instances, seeds coated with
spores could be dried overnight. However, seeds coated with vegetative cultures were
typically stored away before they completely desiccated. Viability test performed
WO 16361
ically on the microbes used in seed coating formulation showed that the es
remained viable for at least three months. Germination rate ofthe coated seeds was
determined to be essentially identical to control uncoated seeds.
EXAMPLE 8: Effect of microbial seed treatments on the development of Fusarium head
blight in wheat
Seeds of a FHB-susceptible wheat cultivar (RB07) were coated with each ofthe
microorganisms SGI-014—C06; SGI—OlS-F03, and SGI-OlS-HOG, in accordance with the
procedure described in Example 8. Coated seeds were subsequently sown in one-liter pots
containing pasteurized soil medium [(Metromix—Mix 200; -Sierra Horticultural
Products, ille, OH; and 3 gram of fertilizer 14—14—14 (N-P—K)]. Pots were seeded at
7-8 plants per pot and subsequently thinned to 5 plants per pot at the 3—leaf stage. Pots were
ed in randomized blocks with 5 pots per treatments. The coated seeds were then
allowed to germinate in ouse conditions under fluorescent ng with 16 hours of
lighting per day. At the onset of wheat flowering (anthesis), the wheat heads were challenged
by spraying with F. graminearum NRRL 5883 macroconidial spores at a concentration of
100,000 spores/mL. After spraying spores, wheat plants were transferred to a dew chamber
with 100% ty for three days to allow for infection. The treatments were:
1. Untreated: no microbial or chemical fungicide treatment + Fusarz'um challenge.
2. SGIC06: bacterial seed treatment + Fusarium challenge.
3. SGI—Ol 5-F03: bacterial seed treatment + Fusarium challenge.
4. SGI-OlS-H06: bacterial seed treatment + Fusarium challenge.
Severity of head blight disease was ed visually at ten days and twenty-one
days after infection. Disease severity was determined for each spike showing head blight
disease symptoms, and calculated as the percentage of matic spikelets; i. e. the number
of spikelets displaying FHB symptoms divided by the total number of spikelets. The results
(TABLE 5) revealed that wheat seeds coated with each of the three ial antagonists
tested, SGIC06; SGI-OlS—FO3, and SGI-OlS-H06, had significantly lower severity of
Fusarz'um graminearum infestation when compared to the ated” control growing in the
same conditions (P<0.05).
Table 5: Development of head blight symptoms in wheat following seed treatments with
antagonistic microorganisms
_10 days post-infection
SGI-014—C06 2.08
S-F03 23.12
E 9: Biocontrol ofhead-blight disease of wheat in greenhouse trials
Each of the microorganisms SGICO6; SGI—OlS-FO3, and SGI—OlS-H06 were
further tested at larger-scale greenhouse trials. The trials were conducted in a “plant growth
containment room” (PGCR) located at Synthetic Genomics, Inc., and included the following
control treatments: infected control, fected control, as well as four commercial
fungicide benchmarks. The benchmarking chemical fungicides were Banner MAXX®
(Syngenta) at a concentration of 2 ml/L and Prosaro® (Bayer CropScience) at a concentration
of 3 ml/L, each applied as a foliar spray, following manufacturers’ recommendation. The
benchmarking biological firngicides were Actinovate® al Industries) and RhizoVital®
(ABiTEP GmbH), each applied as a soil drench as per instruction s recommended by
manufacturers.
The microbial treatments were prepared and applied either as a soil drench or as a
seed coat. When ial treatments were applied as a soil drench, cell suspensions of each
of the microorganisms were individually applied to the seeds before covering the seeds with
more growth medium. For this purpose, freshly prepared cultures were pelleted to remove
growth media and resuspended in 10 mM ium sulfate (MgSO4) buffer. Cell
suspensions were then added by ing and buting 20 milliliters evenly across the
seeds at a total cell number of ~1 09 cells per pot. When microbial treatments were applied as
a seed coating, microorganism cells/spores were essentially ed as described in Example
8 above. Coated seeds were produced by incorporating cell suspensions with a gum Arabic
solution to form a tacky coating mixture that was subsequently applied to the seeds. The
microbial seed coating was then allowed to dry to form a hard but water soluble biopolymer
entrapping the rganism cells/spores. The goal was to reach a cell titer in the range of at
least 106 — 107 viable cells/seed. In this greenhouse trial ment, the seed coatings were
prepared the day prior to the sowing ofthe seeds.
Each treatment had four replicates that were positioned in a Randomized Complete
Block Design (RCBD) on three leveled racks arranged in two rows along the sides of a
growth room. The racks were ed with fluorescent lights (Agrosun, 5850K) that
generated on average 800 umole of light intensity as measured at the pot surface. Each
replicate consisted of four l-liter pots contained in a half flat. The pots were filled with a
synthetic growth medium consisted of a 3:1 ratio (V/v) of Arabidopsis Growth Medium AIS
(Lehle Seeds) to sand (Washed Coarse). In each pot, two grams of spring wheat seeds (Hank,
WestBred) were scattered on the surface ofthe growth medium. The pots were bottom
watered by keeping ~2 cm water at their base and ed for germination and growth.
At ng stage (Feekes ) the wheat heads were infected by spraying with
a Fusarium gramz'nearum conidial spore suspension. For this greenhouse trial experiment,
fungal spores were prepared by plating homogenized mycelia ofF. gramz'nearum strain
NRRL 5883 onto large PDA plates, followed by five-day incubation under constant light at
room temperature. The fungal spores were then harvested by flooding the plates with
magnesium sulfate buffer (10 mM MgSO4; 0.01% Tween 20) and gently scraping the agar
e with a sterile spatula. The spore concentration was adjusted and approximately
50,000 conidial spores were applied per head with a pressurized hand sprayer. The growth
room ve humidity was increased to 90% for three days allowing for ion before
again being normalized. After wheat seeds had set, watering was d and the wheat
heads were allowed to dry completely. Individual wheat heads were ted and collected.
Disease severity was determined for each wheat head showing head blight disease symptoms.
Disease severity was calculated as the number of diseased spikelets divided by the total
number of spikelets per head. The results (TABLE 6) revealed that wheat treated with each
ofthe three microbial antagonists tested, SGIC06; SGI-OlS-F03, and SGI-OlS-HO6, had
significantly lower severity and incidence ofFusarz'um graminearum infestation when
compared to the “untreated” l growing in the same conditions (P<0.05).
TABLE 6. Efficacy of the microbial antagonists in reducing head blight incidence in wheat.
Infection severity (%) Infection protection%
——-u-
SGI-OlS-H06 26.6 i 7.4 34.00
To determine seed yield, wheat heads were individually threshed by hand, the
seeds collected and d of chaff and other detritus, counted, and d. The total seed
yield was determined as the total seed mass produced by 16 pots of each ofthe treatments.
As reported in TABLE 7 each ofthe three microbial nists tested was found to
significantly protect the seed yield; 1'. e. the yield loss caused by head blight infestation was
significantly reduced.
TABLE 7. Efficacy ofthe microbial antagonists in preserving seed yield in wheat plants
having head blight disease.
——-a-
SGI—OlS-FO3
S-H06
Thus, treatments of wheat plants with each of the tested microorganisms
significantly preserved the wheat plants t yield loss caused by Fusarz‘um infestation. In
particular, wheat plants treated with either SGI—014-C06 or SGI-OlS-F03 showed a
significant improvement in total seed yield; z'.e. 110% and 120% respectively, when
compared to non-infected control. In contrast, the benchmarking fungicides Actinovate®,
RhizoVital®, and Prosario® did not appear to significantly protect the treated Wheat plants
from yield loss caused by Fusarium head blight infestation.
E 10: Biocontrol ofwheat scab under field conditions.
Microorganism antagonists that were found having suppressive activity t the
en F. graminearum and head blight disease in in vitro antagonism assays and
greenhouse studies, as described in Examples 4-9, are further evaluated in a series field
experiments at ent geographical locations throughout the United States. Some
experiments are carried out in agricultural areas which are used for iological control of
wheat scab, where natural disease infection occurs. The wheat variety used in the test is a F.
graminearum susceptible variety. Generally, Wheat plants with each treatment were sown in
plots of 12 rows, about 3-meters long. The space between rows is about 20 cm. Treated
plots in each ment are arranged in a randomized block design. The efficacy of various
wettable powder itions containing the microbial antagonists ofthe present invention
in reducing head blight severity and incidence are also assessed. In these experiments, the
microbial antagonists are evaluated either individually or in combination.
In these tests, microorganism antagonists are evaluated in various seed-coating
treatments and/or field tests where microbial suspensions are applied directly onto ng
wheat heads. In each ofthe experiments, the microorganisms are assessed in replicated plots.
Antagonist, en, and plant production methods as described in Examples 4 -9 can be
used in these experiments.
Seed-coating treatment — In on to the seed coating method described in
Example 7 above, a variety oftechniques and seed-coating ations known in the art can
be deployed for the treatment ofwheat seeds with microbial antagonists, such as those
described usly by Fernando et al., 2002; Bello et al.
, 2002; and Kim et al, 1997. In
general, wheat seeds are pre-moistened and stored at room temperature to promote
ation. ated seeds can be then immersed into microbial sions before
seeding. The pathogen spores can be inoculated either before or after bacterial inoculation.
Antagonist, pathogen, and plant production methods as described in Examples 4 and 5 can be
used for these seed treatments.
Disease severity and yield assessment — The antagonists are subjected to further
evaluation in greenhouse and field evaluation for their suppressive activity against head
blight disease on wheat and barley at ng stages, by using a variety of methods and
procedures, typically those described in, e.g., Schisler, Plant Disease, Vol 86(12), 1350—1356,
2002; Schisler et al. Biological Control, 39:497—506, 2006; and Khan and Doohan, Biological
l, 48:42-47, 2009. In one of such experiments, inoculums of G. zeae are prepared on
sterile, yellow dent corn as described by Khan et al. (Biological Control, 29:245-255, 2004).
Fully colonized lipid cultures ur culture) of microbial strains are diluted to one-quarter
strength with ate buffer. Final CFU per mL counts for antagonist treatments are
between 1 X 109 CFU/mL and 6 X 109 CFU/mL. Treatment suspensions are then applied to
flowering wheat heads using a C02 backpack sprayer. Treatments are typically d after
sunset to minimize potential UV degradation of antagonist cells. There are 5 replicates per
treatment which are arranged in a randomized block . The primary control treatment
consists of plants treated with a buffer solution. A second control consists of untreated
plants. Field assessments of head blight e and incidence are made by evaluating 60
heads per ate (i. e. 300 heads/treatment) When plant development reaches n mid-
milk and soft dough development. Wheat heads are harvested by hand and threshed using an
Almaco single plant and head thresher (Almaco, IA) when grains reach full maturity. Grain
samples obtained fiom each replicate row are evaluated for lOO—kernel weight. Disease
severity, incidence, and 100-kernel weight data are ed using one-way analysis of
variance (ANOVA).
The compositions containing the microbial antagonists ofthe invention, either
individually or in combination, are found to significantly diminish the disease incidence.
These results show that the biological control measures using these active microbial agents
can play an important role in the management of scab on cereal plants such as wheat .
EXAMPLE 11: Development ofnon-naturally occurring cultivars and breeding program
Endophytic microorganisms ofthe present ion are introduced into crop
plants, including s, of varying genotypes and geographic origin, lacking such
endophytic rganisms, to create plant-endophyte combinations with improved
agronomic characteristics, using procedures analogous to those known in the art, including
those described in US. Pat. Appl. No. 20030195117A1; US. Pat. Appl. No.
20010032343A1; and U.S. Pat. No. 7,084,331, among others. Thus, given synthetic plant-
endophyte combinations may be created and selected in a breeding/cultivar pment
program based on their ability to form and maintain a mutualistic combination that results in '
an agronomic benefit. Rating of agronomic characteristics of the combination may also be
utilized in such a breeding m. These characteristics may include, without limitation,
drought tolerance, biomass accumulation, resistance to insect infestation, palatability to
livestock (e.g. herbivores), ease of reproduction, and seed yield, among others. Such
combinations may differ in levels of accumulation of microbial metabolites that are toxic to
pests and weeds, including ergot alkaloid levels, loline levels, peramine levels, or lolitrem
levels, while displaying desired agronomic characteristics of crop plants, including resistance
to insect g or infestation, resistance to abiotic stress, palatability to ock, biomass
accumulation, ease of reproduction, and seed yield, among other traits.
A number ofembodiments of the ion have been described. Nevertheless, it
will be understood that elements of the embodiments described herein can be combined to
make additional embodiments and various modifications may be made without departing
from the spirit and scope of the invention. Accordingly, other embodiments, alternatives and
equivalents are within the scope of the invention as described and claimed herein.
Headings within the application are solely for the convenience of the , and
do not limit in any way the scope of the ion or its embodiments.
All publications and patent applications ned in this specification are herein
incorporated by reference to the same extent as if each individual publication or patent
application was specifically can individually indicated to be incorporated by reference.
5555
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RECOGNITION OF THE DEPOSIT OF MICROORGANISMS
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1 1149 North Torrey Pines Rd. identified at the bottom of this page
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The microorganism identified under I. above was accompanied by:
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byit on (date of receipt of request for conversion).
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INTERNATIONAL FORM
TO RECEIPT IN THE CASE OF AN ORIGINAL DEPOSIT
Patent Dept. issued nt to Rule 7.1 by the
Synthetic Genomics INTERNATIONAL DEPOSITARY ITY
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Patent Dept.
Synthetic cs, Inc. issued pursuant to Rule 10.2 by the
11149 North Torrey Pines Rd. INTERNATIONAL TARY AUTHORITY
La Jolla, CA 92037 identified at the bottom of this page
NAIVIE AND ADDRESS OF THE PARTY TO WHOM
THE VIABILITY ENT IS ISSUED
I. DEPOSITOR II. IDENTIFICATION OF THE MICROORGANISM
Name: Dr. Spehar Depositor’s taxonomic designation and accession number
Synthetic Genomics, Inc. given by the INTERNATIONAL DEPOSITARY
11149 North Torrey Pines Rd. AUTHORITY
Address: LaJolla, CA 92037 Bari/[m amy/o/z'qmyfim'em
NRRL B—50760
Date of: June 21, 2012
nal Deposit
E] New Deposit
[:1 Repropagation of Original Deposit
III. (a) VIABILITY STATEMENT
Deposit was found:
WViable D zNonviable on une 23 2012 (Date)
International Depositary Authority's preparation was found viable on lune 30, 2012 3
III. . DEPOSITOR'S EOUIVALENCY DECLARATION
Depositor determined the International Depositary Authority's preparation was
% ZEquivalent 2Not equivalent to deposit on (Date)
SignatureofDeposr'tor I‘LL/f /I/Z 91/4”),.,.
IV. IONS UNDER WHICH THE VIABILITY TEST WAS PERFORMED D e ositors/De osita 4
V. INTERNATIONAL TARY AUTHORITY
Name: Agricultural ch Culture Signature(s) of (s) having the power to represent the
Collection (NRRL) International Depositary Autho ‘ty or of authorized official(s):
International Depositary Authority
Address: 1815 N. University Street 2
Peoria, Illinois 61604 U.S.A. Date: 8““ »D
‘ Indicate the date of the original deposit
or when a new deposit has been made.
2 Mark with
a cross the applicable box.
3 In the
cases referred to in Rule 10.2(a)(ii) and (iii), refer to the most recent viability test.
‘ Fill in if the information has been requested.
5959
BUDAPEST TREATY ON THE INTERNATIONAL ITION OF THE DEPOSIT
OF MICROORGANISMS FOR THE PURPOSE OF PATENT PROCEDURES
INTERNATIONAL FORM
VIABILITY STATEMENT
Patent Dept.
Synthetic Genomics, Inc. issued pursuant to Rule 10.2 by the
11149 North Torrey Pines Rd. INTERNATIONAL DEPOSITARY AUTHORITY
Lajolla, CA 92037 identified at the bottom of this page
NAME AND S OF THE PARTY TO WHOM
THE VIABILITY STATEMENT IS ISSUED
I. DEPOSITOR II. IDENTIFICATION OF THE MICROORGANISM
Name: Dr. Spehar Depositor’s taxonomic designation and accession number
Synthetic Genomics, 1110- given by the INTERNATIONAL DEPOSITARY
11149 North Torrey Pines Rd. AUTHORITY
Address: Lajolla, CA 92037 Bad/1m ”(Mi/1';
NRRL B-50761
Date of: June 21, 2012
Original Deposit
New Deposit
El Repropagation of Original Deposit
III. (a) VIABILITY ENT
Eyosit was found:2Viable E] 2Nonviable on une 23 2012 (Date)
International Depositary Authority's preparation was found viable on lune 30, 2012 (Date)3
III. - DEPOSITOR'S EUIVALENCY DECLARATION
Depositor determined the International tary Authority's preparation was
%_ ZEquivalent2Not equivalent to deposit on (Date)
Signature of Depositor ; /
/’ L 0/2
IV. CONDITIONS UNDER WHICH THE VIABILITY TEST WAS PERFORMED I e- 051tors/De .osna
V. INTERNATIONAL DEPOSITARY AUTHORITY
Name: Agricultural Research e Signature(s) of person(s) having the power to represent the
tion (NRRL) International Depositary Au hority or of authorized official(s):
ational Depositary Authority
Address: 1815 N. University Street /
Peoria, Illinois 61604 USA. Date: 310 ‘11,
' Indicate the date of the original deposit or when
a new t has been made.
2 Mark with
a cross the applicable box.
3 In the
cases referred to in Rule 10.2(a)(ii) and (iii), refer to the most recent viability test
4 Fill in if the information has been requested.
SEQUENCE LISTING
<110> SYNTHETIC GENOMICS, INC.
GRANDLIC, CHRISTOPHER J.
GREEN, WAYNE A.
KEROVUO, JANNE S.
MCCANN, RYAN T.
<120> ITIONS AND METHODS FOR CONTROLLING HEAD BLIGHT DISEASE
<130> SGI1520-1WO
<150> US 61/511,467
<151> 201125
<160> 18
<170> PatentIn n 3.5
<210> 1
<211> 1430
<212> DNA
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate 4-C06
<220>
<221> misc_feature
<223> encodes a 16S ribosomal RNA
<400> 1
acgctggcgg cgtgcttaac acatgcaagt cgaacggtga acacggagct tgctctgtgg
gatcagtggc gaacgggtga gtaacacgtg agcaacctgc ccctgactct gggataagcg
ctggaaacgg cgtctaatac tggatatgtg acgtgaccgc atggtctgcg tctggaaaga
atttcggttg ggct cgcggcctat cagcttgttg gtgaggtaat ggctcaccaa
ggcgtcgacg ggtagccggc ctgagagggt gaccggccac actgggactg agacacggcc
cagactccta cgggaggcag cagtggggaa acaa tgggcgcaag cctgatgcag
caacgccgcg tgagggacga cggccttcgg gttgtaaacc tcttttagca gggaagaagc
gaaagtgacg gtacctgcag cgcc ggctaactac gtgccagcag ccgcggtaat
ggcg caagcgttat ccggaattat tgggcgtaaa gagctcgtag tgtc
gcgtctgctg tgaaatccgg aggctcaacc tccggcctgc agtgggtacg ggcagactag
gtag gggagattgg aattcctggt gtagcggtgg aatgcgcaga tatcaggagg
aacaccgatg gcag atctctgggc cgtaactgac gctgaggagc gaaagggtgg
ggagcaaaca ggcttagata ccctggtagt ccaccccgta aacgttggga actagttgtg
gggtccattc cacggattcc gtgacgcagc taacgcatta agttccccgc ctggggagta
cggccgcaag gctaaaactc aaaggaattg acggggaccc gcacaagcgg cggagcatgc
ggattaattc acgc gaagaacctt accaaggctt gacatatacg ggcc
ggtc aactctttgg acactcgtaa acaggtggtg catggttgtc gtcagctcgt
1020
gtcgtgagat gttgggttaa gtcccgcaac gagcgcaacc ctcgttctat gttgccagca
1080
cgtaatggtg ggaactcatg tgcc ggggtcaact aagg tggggatgac
1140
gtcaaatcat catgcccctt atgtcttggg cttcacgcat gctacaatgg ccggtacaaa
1200
gggctgcaat accgcgaggt ggagcgaatc ccaaaaagcc ggtcccagtt cggattgagg
1260
tctgcaactc gacctcatga agtcggagtc gctagtaatc cagc aacgctgcgg
1320
tgaatacgtt cccgggtctt gtacacaccg aagt catgaaagtc ggtaacacct
1380
gaagccggtg gcctaaccct tgtggaggga gccgtcgaag gtgggatcgg
1430
<210> 2
<211> 2172
<212> DNA
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate 4-C06
<220>
<221> misc_feature
<223> SGI Gene ID SG1MICG850682
<220>
<221> misc_feature
<223> encodes the e sequence at SED ID NO 3
<400> 2
gtgtctgcgg ccggagagcg gctgtcgaga atagactcgg agattgtgaa tgccgagtat
tccgcccatc atctccaggt gcttgagggg ctcgaagctg tccgcaagcg cccgggcatg
tacatcgggt cgaacggctc gccgggcctc atgcactgcc tttgggagat catcgacaac
tctgtcgacg aggcggtggc aggcaacggc acgaagatcg acatcatcct gcactccgac
ggcagcgtcg aggtgcacga tcgc ggcatccctg tcgacgtcga gccgcgcacc
ggtctcaccg gtgtcgaggt cgtctacacc aagctgcacg ccggaggaaa gttcggcggc
ggctcgtacg cggcatccgg tggactgcac ggtgtcggcg cctccgtcgt gaacgcgctc
tccgagcgcc tcgacgtcga ggtcgaccgc gggggcaaga cctacgcgat gtcgttccat
cgcggtgagc ccggcatctt cacggactcc ggcgagaagc ggccggacgc cccgttcacg
ccgttcgagg agaacagcga gctgcgcgtc atcggcaagg cgccgcgtgg cgtgaccggc
acccgggtgc gctactgggc cgaccggcag atcttcacca cggc gttccagctc
tcggagctcg gcgc gacg gcgttcctcg ttcccggtct cgagatcgtc
gtcaaggacg cacgggcggc ggtc atccccgtcc ccga cggcgagacg
accgtcgtcg atga gacctcgtac ctctacgagg gcggcatctc cgagttcgtc
gagtacctcg ccatcgaccc tcccgtgacc gacacctggc gtatccaggg cgagggcatg
ttcaaggaga ccgt cctgcaggca gacggccaca tggtcgccac ggag
cgtgtgtgcg ccgtcgacat cgcgctgcgc tgggggaccg gctacgacac ccgtgtgcgc
1020
tccttcgtga acatcatcgc gacgcccaag ggcggaaccc accagcaggg cttcgagcag
1080
ctga aggtgctgcg ctcccaggtc gagcagaacg cccgccgtct gaaggtcggc
1140
aacgacaagc tggagaagga cgacgtcctc gccggcctca ccgccgtgct cacggtcaac
1200
gtgccggagc cgcagttcga gggccagacc aaggaagtgc tcggcacccc cgcggtgcgg
1260
cagatcgtgg cgcaggtgat ccgtaaggat ctggcgcagc gctc gaccaagcgc
1320
gacgacaaga accaggccac acagctgctc gacaagatcg tctccgagat gaaggcccgt
1380
gcgc gcgcccacaa ggagacgcag cgccgcaaga acgcgctgga gtcgtcgacg
1440
ctgccgacca agctcgtcga ctgccgcacg gtcg gcga gctcttcatc
1500
gtggagggcg actcggctct cggcaccgcc aagaacgcgc gcaacagcga gttccaggcg
1560
ctgctcccga tccgagggaa gatcctcaac aagg cctctgtcgg cgacatgctg
1620
tcgaacaccg agtgcgcgtc gatcatccag gtgatcggcg ccggatccgg acgcaccttc
1680
gacatcgatg cggcgcgcta cggcaaggtg atcctgatga gcgacgccga tgtcgacggc
1740
gcgcacatcc gtaccctgct gctcacgctg ttcttccgct acatgcgacc gctgatcgag
1800
cacgggcgtg tgttcgccgc ggtgccgccg ttgcaccggg tgatcgtgat gaacccgggg
1860
tccaagccga cgat ctacacctac agcgagcagg acgc gctgctggcg
1920
aagctccgca aggccggcaa gcgctggcac gagccgatcc agcgctacaa gggtctcggt
1980
gagatggacg cggaacagct cgcgaacacc accatggacc gctccggccg tctgctgcgc
2040
cgtgtgcgca tggaagacgc cgaggccgcc ggtcgcgtgt tcgagctgct gatgggcaac
2100
gaggtcgcgc cgcgccgcga gttcatcatc gactcctccg accggttgtc gtcc
2160
atcgacgcct ga
2172
<210> 3
<211> 723
<212> PRT
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIC06
<220>
<221> misc_feature
<223> SGI peptide ID SG1MICT850682
<220>
<221> misc_feature
<223> gyrase subunit B
<400> 3
Met Ser Ala Ala Gly Glu Arg Leu Ser Arg Ile Asp Ser Glu Ile Val
1 5 10 15
Asn Ala Glu Tyr Ser Ala His His Leu Gln Val Leu Glu Gly Leu Glu
25 30
Ala Val Arg Lys Arg Pro Gly Met Tyr Ile Gly Ser Asn Gly Ser Pro
40 45
Gly Leu Met His Cys Leu Trp Glu Ile Ile Asp Asn Ser Val Asp Glu
50 55 60
Ala Val Ala Gly Asn Gly Thr Lys Ile Asp Ile Ile Leu His Ser Asp
65 70 75 80
Gly Ser Val Glu Val His Asp Arg Gly Arg Gly Ile Pro Val Asp Val
85 90 95
Glu Pro Arg Thr Gly Leu Thr Gly Val Glu Val Val Tyr Thr Lys Leu
100 105 110
His Ala Gly Gly Lys Phe Gly Gly Gly Ser Tyr Ala Ala Ser Gly Gly
115 120 125
Leu His Gly Val Gly Ala Ser Val Val Asn Ala Leu Ser Glu Arg Leu
130 135 140
Asp Val Glu Val Asp Arg Gly Gly Lys Thr Tyr Ala Met Ser Phe His
145 150 155 160
Arg Gly Glu Pro Gly Ile Phe Thr Asp Ser Gly Glu Lys Arg Pro Asp
165 170 175
Ala Pro Phe Thr Pro Phe Glu Glu Asn Ser Glu Leu Arg Val Ile Gly
180 185 190
Lys Ala Pro Arg Gly Val Thr Gly Thr Arg Val Arg Tyr Trp Ala Asp
195 200 205
Arg Gln Ile Phe Thr Lys Asp Ala Ala Phe Gln Leu Ser Glu Leu Glu
210 215 220
Thr Arg Ala Arg Gln Thr Ala Phe Leu Val Pro Gly Leu Glu Ile Val
225 230 235 240
Val Lys Asp Ala Arg Ala Ala Gly Gln Val Ile Pro Val Pro Asp Ser
245 250 255
Asp Gly Glu Thr Thr Val Val Gly Thr Asp Glu Thr Ser Tyr Leu Tyr
260 265 270
Glu Gly Gly Ile Ser Glu Phe Val Glu Tyr Leu Ala Ile Asp Pro Pro
275 280 285
Val Thr Asp Thr Trp Arg Ile Gln Gly Glu Gly Met Phe Lys Glu Thr
290 295 300
Val Pro Val Leu Gln Ala Asp Gly His Met Val Ala Thr Glu Val Glu
305 310 315 320
Arg Val Cys Ala Val Asp Ile Ala Leu Arg Trp Gly Thr Gly Tyr Asp
325 330 335
Thr Arg Val Arg Ser Phe Val Asn Ile Ile Ala Thr Pro Lys Gly Gly
340 345 350
Thr His Gln Gln Gly Phe Glu Gln Glu Leu Leu Lys Val Leu Arg Ser
355 360 365
Gln Val Glu Gln Asn Ala Arg Arg Leu Lys Val Gly Asn Asp Lys Leu
370 375 380
Glu Lys Asp Asp Val Leu Ala Gly Leu Thr Ala Val Leu Thr Val Asn
385 390 395 400
Val Pro Glu Pro Gln Phe Glu Gly Gln Thr Lys Glu Val Leu Gly Thr
405 410 415
Pro Ala Val Arg Gln Ile Val Ala Gln Val Ile Arg Lys Asp Leu Ala
420 425 430
Gln Arg Phe Ser Ser Thr Lys Arg Asp Asp Lys Asn Gln Ala Thr Gln
435 440 445
Leu Leu Asp Lys Ile Val Ser Glu Met Lys Ala Arg Val Ser Ala Arg
450 455 460
Ala His Lys Glu Thr Gln Arg Arg Lys Asn Ala Leu Glu Ser Ser Thr
465 470 475 480
Leu Pro Thr Lys Leu Val Asp Cys Arg Thr Asn Glu Val Glu Arg Ser
485 490 495
Glu Leu Phe Ile Val Glu Gly Asp Ser Ala Leu Gly Thr Ala Lys Asn
500 505 510
Ala Arg Asn Ser Glu Phe Gln Ala Leu Leu Pro Ile Arg Gly Lys Ile
515 520 525
Leu Asn Val Gln Lys Ala Ser Val Gly Asp Met Leu Ser Asn Thr Glu
530 535 540
Cys Ala Ser Ile Ile Gln Val Ile Gly Ala Gly Ser Gly Arg Thr Phe
545 550 555 560
Asp Ile Asp Ala Ala Arg Tyr Gly Lys Val Ile Leu Met Ser Asp Ala
565 570 575
Asp Val Asp Gly Ala His Ile Arg Thr Leu Leu Leu Thr Leu Phe Phe
580 585 590
Arg Tyr Met Arg Pro Leu Ile Glu His Gly Arg Val Phe Ala Ala Val
595 600 605
Pro Pro Leu His Arg Val Ile Val Met Asn Pro Gly Ser Lys Pro Asn
610 615 620
Glu Thr Ile Tyr Thr Tyr Ser Glu Gln Glu Met His Ala Leu Leu Ala
625 630 635 640
Lys Leu Arg Lys Ala Gly Lys Arg Trp His Glu Pro Ile Gln Arg Tyr
645 650 655
Lys Gly Leu Gly Glu Met Asp Ala Glu Gln Leu Ala Asn Thr Thr Met
660 665 670
Asp Arg Ser Gly Arg Leu Leu Arg Arg Val Arg Met Glu Asp Ala Glu
675 680 685
Ala Ala Gly Arg Val Phe Glu Leu Leu Met Gly Asn Glu Val Ala Pro
690 695 700
Arg Arg Glu Phe Ile Ile Asp Ser Ser Asp Arg Leu Ser Arg Glu Ser
705 710 715 720
Ile Asp Ala
<210> 4
<211> 3504
<212> DNA
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI ial isolate SGIC06
<220>
<221> misc_feature
<223> SGI Gene ID SG1MICG850290
<220>
<221> eature
<223> encodes the peptide sequence at SEQ ID NO 5
<400> 4
ttggctgctg acgc atccacatcc accaccacca agaacggacg cggagcttcc
cgtctttcgt tcgccaagat ctccgacacg ctgacggtcc ctgaccttct gcag
accgaatcct tcggttggct ggtcggcaac tgga gcgt ggccgaggcc
aagaagcagg ggcgcaccga cgtcaacgag aacagcggtc tgggcgagat cttcgaggag
atctctccga tcgaggacct gacg atgcagctgt cgttcacgaa cccctacctc
gaga agtactccat cgaggagtgc aaggagcgtg gcaagaccta cgccgctccg
ctgtacgtcg aggccgagtt catgaaccac ctcacgggtg agatcaagac ccagacggtc
ttcatgggcg cgct gcagaccgac acgt tcatcatcaa cggctccgag
cgcgtcgtcg agct ggtgcgttcg cccggtgtct acttcgacaa gacccccgac
aagacgtccg acaaggacat cgtctcggca cgcgtcatcc cgagccgtgg tgcctggctc
gagttcgaga tcgacaagcg cgaccaggtc ggcgtgcgcg tcgaccgcaa gcgcaagcag
tcggtcacgg tcttcctcaa ggcgctgggc atgaccagcg aggagatcct cgccgagttc
gccggctaca cctcgatcga ggagacgctc gcgaaggaca tcac gaaggaagat
gcgctccgcg acatctaccg caagctccgt ccgggcgagc aggtcgccgc cgaggccgcc
cgcgcgctcc tggacaactt ctacttcaac ccgaagcgct acgacctggc caaggtcggt
cgctacaaga tcaaccacaa gctgggcctg gaccagccgc tgaactcgtc ggtcctgacc
gtcgaagaca tcgtggccac gatcaagtac ctggtgcgtc tgcacgccgg caccgaggag
1020
accttcacgg gcatccgcgg tggtaagaag gccgagatcc gtctcgcgac cgacgacatc
1080
gacaacttcg gcaaccgtcg catccgcgcg gtcggcgagc tgatccagaa ccaggtccgc
1140
accggtctct tgga gcgcgtcgtc cgcgagcgca cgca ggacatcgag
1200
gcgatcacgc cgcagaccct gatcaacgtg cgccccgtcg tcgccgcgat caaggagttc
1260
ttcggaacgt cgcagctgtc gcagttcatg gaccagaaca acccgctcgc gggtctgacg
1320
aacaagcgtc gtctgtctgc gctcggcccc ggtggtctct cgcgagaccg cgccggcgtc
1380
gaggtccgtg acgtccaccc ctcgcactac ggccgcatgt gcccgatcga gactccggaa
1440
ggcccgaaca tgat cggtgctctc gcgaccttcg cgcgcatcaa cgga
1500
ttcatcgaga ccccgtaccg caaggtcgtc gacggtgtcg tgaccgacca gatcgactac
1560
ctgacggctt ccgaagaggt cgacttcaac atcgcgcagg cccc gctcgatgcc
1620
aagggtcgct tccgcgagag ccacgtcctg ccca agggtggcag cggcgaggtc
1680
gacctgttcg tccccgagga gatcggctac atcgacgtct ccccgcgcca gatggtgtcg
1740
gtcgcgacct cgctcgtgcc cttcctcgag cacgacgacg cacagcgcgc cctcatgggt
1800
gccaacatgc agcgtcaggc tgtgccgctg ctgcgcagcg actcgccgct cgtcggaacc
1860
ggtatggagg gctacacggc catcgacgcc ggtgacgtgc tcaccgccga gaaggccggt
1920
gtcgtctccg aggtctccgc agaccgcgtc gtcgtcatgc tcgacgaggg gcag
1980
gagtaccacc tgcgcaagtt cgaccgctcc aaccagggca cgtcgtacaa ccagaaggtc
2040
gtcgtcaccg ccggtgagcg cgtcgaggtc ggagaggtca tcgccgatgg ccccgccacc
2100
gagaacggcg agctggccct cggaaagaac gtcg cgttcatgac gtgggagggc
2160
tacaacttcg aggacgcgat catcctgagc caggacctgg tgaaggacga ctcc
2220
tcgatccaca agta cgaggtcgat gctcgcgaca ccaagctcgg caaggaggag
2280
atcacgcgtg acctccccaa cgtcagcccg gagctgctga aggacctcga cgagcgcggc
2340
atcatccgca ccga ggtccgccct ggcgacatcc tcgtcggcaa ggtcacgccg
2400
aagggtgaga ccgagctgtc ggccgaggag cgcctgctcc gcgcgatctt caacgagaag
2460
agccgcgaag tccgtgacac ctcgctgaag gtgccccacg gtgagcaggg catc
2520
gccgtcaagg agttcaacgc tgaggacggc gacgacgagc tcggctccgg cgtcaaccgc
2580
cgcgtcgtgg tctacatcgc ccagaagcgc aagatcaccg agggtgacaa gctcgccggc
2640
cgtcacggca acaagggtgt catcgcgaag atcctcccga tcgaggacat gccgttcctt
2700
tcggacggta ccccggtcga catcgtgctg aacccgctcg gtatccccgg tcgaatgaac
2760
ttcggtcagg tcctggagac cggg tggatcgcga agcagggctg gaaggtcgag
2820
ggcaacccgg agtgggctgt cccg aaggacgcat tcgaggccgc ccccggcacg
2880
gcca ccccggtgtt cgacggtgcg agcgaggagg agatcgctgg tctcctcgac
2940
gcgaccaccc cgacccgtga cggcgtccgc ctgatcgact cgagcggcaa gacgcagctg
3000
ttcgacggtc gttcgggtga gccgttcccg gcgccgatct ccgtgggcta catgtacatc
3060
ctgc accacctggt cgacgacaag atccacgcac gttccacggg tccgtactcg
3120
atgatcaccc agcagccgct cggtggtaag gcgcagttcg gtggacagcg cttcggtgag
3180
atggaggtgt gggccctcga ggcctacggc gccgcatacg cgctccagga gctcctcacg
3240
atcaagtccg acgacatcct cggccgcgtc aaggtgtacg tcgt caagggcgag
3300
aacatccagg agcccggcat gtcg ttcaaggtgc tcatgaagga gatgcagtcg
3360
ctctgcctga acgtcgaggt cctctcggcc gacggcacgc tggtcaacct ccgcgacacc
3420
gagg cgttccgcgc cgcggaagag atca ccag ccgcttcgag
3480
gccgcctcga agat ctaa
3504
<210> 5
<211> 1167
<212> PRT
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIC06
<220>
<221> misc_feature
<223> SGI peptide ID T850290
<220>
<221> misc_feature
<223> RNA-polymerase subunit B
<400> 5
Met Ala Ala Ala Arg Asn Ala Ser Thr Ser Thr Thr Thr Lys Asn Gly
1 5 10 15
Arg Gly Ala Ser Arg Leu Ser Phe Ala Lys Ile Ser Asp Thr Leu Thr
25 30
Val Pro Asp Leu Leu Ala Leu Gln Thr Glu Ser Phe Gly Trp Leu Val
40 45
Gly Asn Asp Ala Trp Lys Ala Arg Val Ala Glu Ala Lys Lys Gln Gly
50 55 60
Arg Thr Asp Val Asn Glu Asn Ser Gly Leu Gly Glu Ile Phe Glu Glu
65 70 75 80
Ile Ser Pro Ile Glu Asp Leu Gly Glu Thr Met Gln Leu Ser Phe Thr
85 90 95
Asn Pro Tyr Leu Glu Pro Glu Lys Tyr Ser Ile Glu Glu Cys Lys Glu
100 105 110
Arg Gly Lys Thr Tyr Ala Ala Pro Leu Tyr Val Glu Ala Glu Phe Met
115 120 125
Asn His Leu Thr Gly Glu Ile Lys Thr Gln Thr Val Phe Met Gly Asp
130 135 140
Phe Pro Leu Gln Thr Asp Lys Gly Thr Phe Ile Ile Asn Gly Ser Glu
145 150 155 160
Arg Val Val Val Ser Gln Leu Val Arg Ser Pro Gly Val Tyr Phe Asp
165 170 175
Lys Thr Pro Asp Lys Thr Ser Asp Lys Asp Ile Val Ser Ala Arg Val
180 185 190
Ile Pro Ser Arg Gly Ala Trp Leu Glu Phe Glu Ile Asp Lys Arg Asp
195 200 205
Gln Val Gly Val Arg Val Asp Arg Lys Arg Lys Gln Ser Val Thr Val
210 215 220
Phe Leu Lys Ala Leu Gly Met Thr Ser Glu Glu Ile Leu Ala Glu Phe
225 230 235 240
Ala Gly Tyr Thr Ser Ile Glu Glu Thr Leu Ala Lys Asp Thr Ile Val
245 250 255
Thr Lys Glu Asp Ala Leu Arg Asp Ile Tyr Arg Lys Leu Arg Pro Gly
260 265 270
Glu Gln Val Ala Ala Glu Ala Ala Arg Ala Leu Leu Asp Asn Phe Tyr
275 280 285
Phe Asn Pro Lys Arg Tyr Asp Leu Ala Lys Val Gly Arg Tyr Lys Ile
290 295 300
Asn His Lys Leu Gly Leu Asp Gln Pro Leu Asn Ser Ser Val Leu Thr
305 310 315 320
Val Glu Asp Ile Val Ala Thr Ile Lys Tyr Leu Val Arg Leu His Ala
325 330 335
Gly Thr Glu Glu Thr Phe Thr Gly Ile Arg Gly Gly Lys Lys Ala Glu
340 345 350
Ile Arg Leu Ala Thr Asp Asp Ile Asp Asn Phe Gly Asn Arg Arg Ile
355 360 365
Arg Ala Val Gly Glu Leu Ile Gln Asn Gln Val Arg Thr Gly Leu Ser
370 375 380
Arg Met Glu Arg Val Val Arg Glu Arg Met Thr Thr Gln Asp Ile Glu
385 390 395 400
Ala Ile Thr Pro Gln Thr Leu Ile Asn Val Arg Pro Val Val Ala Ala
405 410 415
Ile Lys Glu Phe Phe Gly Thr Ser Gln Leu Ser Gln Phe Met Asp Gln
420 425 430
Asn Asn Pro Leu Ala Gly Leu Thr Asn Lys Arg Arg Leu Ser Ala Leu
435 440 445
Gly Pro Gly Gly Leu Ser Arg Asp Arg Ala Gly Val Glu Val Arg Asp
450 455 460
Val His Pro Ser His Tyr Gly Arg Met Cys Pro Ile Glu Thr Pro Glu
465 470 475 480
Gly Pro Asn Ile Gly Leu Ile Gly Ala Leu Ala Thr Phe Ala Arg Ile
485 490 495
Asn Ser Phe Gly Phe Ile Glu Thr Pro Tyr Arg Lys Val Val Asp Gly
500 505 510
Val Val Thr Asp Gln Ile Asp Tyr Leu Thr Ala Ser Glu Glu Val Asp
515 520 525
Phe Asn Ile Ala Gln Ala Asn Ala Pro Leu Asp Ala Lys Gly Arg Phe
530 535 540
Arg Glu Ser His Val Leu Ala Arg Pro Lys Gly Gly Ser Gly Glu Val
545 550 555 560
Asp Leu Phe Val Pro Glu Glu Ile Gly Tyr Ile Asp Val Ser Pro Arg
565 570 575
Gln Met Val Ser Val Ala Thr Ser Leu Val Pro Phe Leu Glu His Asp
580 585 590
Asp Ala Gln Arg Ala Leu Met Gly Ala Asn Met Gln Arg Gln Ala Val
595 600 605
Pro Leu Leu Arg Ser Asp Ser Pro Leu Val Gly Thr Gly Met Glu Gly
610 615 620
Tyr Thr Ala Ile Asp Ala Gly Asp Val Leu Thr Ala Glu Lys Ala Gly
625 630 635 640
Val Val Ser Glu Val Ser Ala Asp Arg Val Val Val Met Leu Asp Glu
645 650 655
Gly Gly Thr Gln Glu Tyr His Leu Arg Lys Phe Asp Arg Ser Asn Gln
660 665 670
Gly Thr Ser Tyr Asn Gln Lys Val Val Val Thr Ala Gly Glu Arg Val
675 680 685
Glu Val Gly Glu Val Ile Ala Asp Gly Pro Ala Thr Glu Asn Gly Glu
690 695 700
Leu Ala Leu Gly Lys Asn Leu Leu Val Ala Phe Met Thr Trp Glu Gly
705 710 715 720
Tyr Asn Phe Glu Asp Ala Ile Ile Leu Ser Gln Asp Leu Val Lys Asp
725 730 735
Asp Thr Leu Ser Ser Ile His Ile Glu Glu Tyr Glu Val Asp Ala Arg
740 745 750
Asp Thr Lys Leu Gly Lys Glu Glu Ile Thr Arg Asp Leu Pro Asn Val
755 760 765
Ser Pro Glu Leu Leu Lys Asp Leu Asp Glu Arg Gly Ile Ile Arg Ile
770 775 780
Gly Ala Glu Val Arg Pro Gly Asp Ile Leu Val Gly Lys Val Thr Pro
785 790 795 800
Lys Gly Glu Thr Glu Leu Ser Ala Glu Glu Arg Leu Leu Arg Ala Ile
805 810 815
Phe Asn Glu Lys Ser Arg Glu Val Arg Asp Thr Ser Leu Lys Val Pro
820 825 830
His Gly Glu Gln Gly Thr Ile Ile Ala Val Lys Glu Phe Asn Ala Glu
835 840 845
Asp Gly Asp Asp Glu Leu Gly Ser Gly Val Asn Arg Arg Val Val Val
850 855 860
Tyr Ile Ala Gln Lys Arg Lys Ile Thr Glu Gly Asp Lys Leu Ala Gly
865 870 875 880
Arg His Gly Asn Lys Gly Val Ile Ala Lys Ile Leu Pro Ile Glu Asp
885 890 895
Met Pro Phe Leu Ser Asp Gly Thr Pro Val Asp Ile Val Leu Asn Pro
900 905 910
Leu Gly Ile Pro Gly Arg Met Asn Phe Gly Gln Val Leu Glu Thr His
915 920 925
Leu Gly Trp Ile Ala Lys Gln Gly Trp Lys Val Glu Gly Asn Pro Glu
930 935 940
Trp Ala Val Lys Leu Pro Lys Asp Ala Phe Glu Ala Ala Pro Gly Thr
945 950 955 960
Lys Val Ala Thr Pro Val Phe Asp Gly Ala Ser Glu Glu Glu Ile Ala
965 970 975
Gly Leu Leu Asp Ala Thr Thr Pro Thr Arg Asp Gly Val Arg Leu Ile
980 985 990
Asp Ser Ser Gly Lys Thr Gln Leu Phe Asp Gly Arg Ser Gly Glu Pro
995 1000 1005
Phe Pro Ala Pro Ile Ser Val Gly Tyr Met Tyr Ile Leu Lys Leu
1010 1015 1020
His His Leu Val Asp Asp Lys Ile His Ala Arg Ser Thr Gly Pro
1025 1030 1035
Tyr Ser Met Ile Thr Gln Gln Pro Leu Gly Gly Lys Ala Gln Phe
1040 1045 1050
Gly Gly Gln Arg Phe Gly Glu Met Glu Val Trp Ala Leu Glu Ala
1055 1060 1065
Tyr Gly Ala Ala Tyr Ala Leu Gln Glu Leu Leu Thr Ile Lys Ser
1070 1075 1080
Asp Asp Ile Leu Gly Arg Val Lys Val Tyr Glu Ala Ile Val Lys
1085 1090 1095
Gly Glu Asn Ile Gln Glu Pro Gly Ile Pro Glu Ser Phe Lys Val
1100 1105 1110
Leu Met Lys Glu Met Gln Ser Leu Cys Leu Asn Val Glu Val Leu
1115 1120 1125
Ser Ala Asp Gly Thr Leu Val Asn Leu Arg Asp Thr Asp Asp Glu
1130 1135 1140
Ala Phe Arg Ala Ala Glu Glu Leu Gly Ile Asn Ile Ser Ser Arg
1145 1150 1155
Phe Glu Ala Ala Ser Ile Asp Glu Ile
1160 1165
<210> 6
<211> 1188
<212> DNA
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI ial isolate SGIC06
<220>
<221> misc_feature
<223> SGI Gene ID SG1MICG851004
<220>
<221> misc_feature
<223> encodes the e ce at SEQ ID NO 7
<400> 6
ttgccgactc gatgtcggtg gcctctccta cggtggaaaa caagccgaag agccattacg
ccttgtcgga gagttgctcc caaccgggag cgccgcgaca gcctacaggc ggcaccacgc
gcgcagaagg agcacatcat gccatcaccc cgcg agaagtccct cgagaccgcc
ctcgcccaga tcgaccgcca gttcggaaag ggctcggtca tgcggctggg cagcgatgag
cgcgcccccg tcat cggc tccatcgccc tcgc cctcggcgtc
ggaggactcc cgcgtggtcg catcgtcgag atctacggac cggagtcctc cggtaagacg
acgctcaccc tgcacgcgat cgcgaacgca cagcgtgccg gtggcatcgc ggcgttcatc
gacgccgagc acgcgctcga ccccgactac gccgccaagc tcggcgtcga catcgatgcg
ctcctggtct cgcagcccga cacgggtgag caggcgctcg agatcgccga catgctcgtg
cgctccggtg cgatcgacct catc gactccgtcg cggccctcgt gccgcgcgcc
gagatcgagg gcgagatggg tgactcgcac gtcggtctgc aggctcgcct catgtcgcag
gcgctgcgaa agctcaccgg tggtctgaac cagacgaaca ccacgatgat cttcatcaac
cagctccgcg agaagatcgg tgtcttcttc ggttcgccgg agaccactgc cggcggtaag
gcgctcaagt tctacgcctc ggtccgcatg gacatccgtc gtatcgagac gctcaaggac
ggtactgacg ctgtcggtaa ccgcaccagg gtcaaggtcg tcaagaacaa gatggctccg
cctttcaagc aggccgagtt cgacatcctc tacggcgtcg gcatctcgcg cgagggaagc
ctgatcgact tcggtgtcga gcatgcgatc gtcaagaagt cctg gtac
1020
gacggtgacc agctgggtca gggcaaggag aacgcgcgga cgttcctgct caacaacccc
1080
gacatcgcgc tggcgatcga gacgcagatc aagcagaagc tcggcatcgg cggtcccgcc
1140
gcggcgcctg ctgcggcaga cgct gagcgtcgtc cggcctga
1188
<210> 7
<211> 395
<212> PRT
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIC06
<220>
<221> misc_feature
<223> SGI peptide ID SG1MICT851004
<220>
<221> misc_feature
<223> recombinase A
<400> 7
Met Pro Thr Arg Cys Arg Trp Pro Leu Leu Arg Trp Lys Thr Ser Arg
1 5 10 15
Arg Ala Ile Thr Pro Cys Arg Arg Val Ala Pro Asn Arg Glu Arg Arg
25 30
Asp Ser Leu Gln Ala Ala Pro Arg Ala Gln Lys Glu His Ile Met Pro
40 45
Ser Pro Ala Asp Arg Glu Lys Ser Leu Glu Thr Ala Leu Ala Gln Ile
50 55 60
Asp Arg Gln Phe Gly Lys Gly Ser Val Met Arg Leu Gly Ser Asp Glu
65 70 75 80
Arg Ala Pro Val Ala Val Ile Pro Thr Gly Ser Ile Ala Leu Asp Val
85 90 95
Ala Leu Gly Val Gly Gly Leu Pro Arg Gly Arg Ile Val Glu Ile Tyr
100 105 110
Gly Pro Glu Ser Ser Gly Lys Thr Thr Leu Thr Leu His Ala Ile Ala
115 120 125
Asn Ala Gln Arg Ala Gly Gly Ile Ala Ala Phe Ile Asp Ala Glu His
130 135 140
Ala Leu Asp Pro Asp Tyr Ala Ala Lys Leu Gly Val Asp Ile Asp Ala
145 150 155 160
Leu Leu Val Ser Gln Pro Asp Thr Gly Glu Gln Ala Leu Glu Ile Ala
165 170 175
Asp Met Leu Val Arg Ser Gly Ala Ile Asp Leu Ile Val Ile Asp Ser
180 185 190
Val Ala Ala Leu Val Pro Arg Ala Glu Ile Glu Gly Glu Met Gly Asp
195 200 205
Ser His Val Gly Leu Gln Ala Arg Leu Met Ser Gln Ala Leu Arg Lys
210 215 220
Leu Thr Gly Gly Leu Asn Gln Thr Asn Thr Thr Met Ile Phe Ile Asn
225 230 235 240
Gln Leu Arg Glu Lys Ile Gly Val Phe Phe Gly Ser Pro Glu Thr Thr
245 250 255
Ala Gly Gly Lys Ala Leu Lys Phe Tyr Ala Ser Val Arg Met Asp Ile
260 265 270
Arg Arg Ile Glu Thr Leu Lys Asp Gly Thr Asp Ala Val Gly Asn Arg
275 280 285
Thr Arg Val Lys Val Val Lys Asn Lys Met Ala Pro Pro Phe Lys Gln
290 295 300
Ala Glu Phe Asp Ile Leu Tyr Gly Val Gly Ile Ser Arg Glu Gly Ser
305 310 315 320
Leu Ile Asp Phe Gly Val Glu His Ala Ile Val Lys Lys Ser Gly Ser
325 330 335
Trp Tyr Thr Tyr Asp Gly Asp Gln Leu Gly Gln Gly Lys Glu Asn Ala
340 345 350
Arg Thr Phe Leu Leu Asn Asn Pro Asp Ile Ala Leu Ala Ile Glu Thr
355 360 365
Gln Ile Lys Gln Lys Leu Gly Ile Gly Gly Pro Ala Ala Ala Pro Ala
370 375 380
Ala Ala Asp Glu Leu Ala Glu Arg Arg Pro Ala
385 390 395
<210> 8
<211> 2175
<212> DNA
<213> acterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIC06
<220>
<221> misc_feature
<223> SGI Gene ID SG1MICG849768
<220>
<221> misc_feature
<223> encodes the peptide sequence at SEQ ID NO 9
<400> 8
atgtacccca tgatcgatcc cgcactcgcc ggcc acgc cgaagacgac
gacttcgacg agtc tcccgactcc cagctcccgg accaccgcta cctggatcgc
gagctgagct ggctcgcctt caaccagcgc gagc tcgccgagga tccgtcactg
ctcg cgaa cttcctggcg atcttcgcca gcaacctcga cgagttcttc
atggtgcgcg tcgccggcct caagcgccgc atcatgaccg gcctggccgt gccgacgaac
atcggccgct cccccgtcga cgcgctcgcc gacatctccc gcgaagcgca cgccctgcag
ctgcgtcacg ccgaggcctg gacctcgctc cccg ccctggccga ctccggcatc
gagatcacgg actggtccga gctgaccgac gacgagcgct ccggattgtc cgagtacttc
cagctccagg cggt gccg ctcgcggtcg acccggcgca tccgttcccc
tacatctccg gcctgtcgct gaacctcgcg atccgcatcc gcaatgcccg caccgggcgc
caggagttcg cgcgcctcaa ggtgccgccc atgctccccc gcttcgtgga ggtgccgggc
ggcggcgaga tcaagcgctt cctgcgcctg gaggaactga tcgcgaacca cctcggcgac
ctgttccccg gcatggaggt gctcgaccac cacgcgttcc gcctcacccg caacgaagac
gtggagatcg aggaagacga gagcgagaac ctcatccagg aggc cgagctgctg
cgccgtcgat tcggcccgcc gatccgcctc gagatcacgg acgacatgga cgaggtcacg
ctgc tcgtccgcga gctcgacatc accgacctgg aggtctaccg cctccccggt
ccgctcgacc tgcgcggact gttcgatctg tcccgcatcg accgtcccga cctgcgctac
1020
ccgccgcacc tgcccaccac ggccgtggcc ttccagcccg caggatcgag caaccgcgcc
1080
ttca aagcgatccg caagtcggat gtgctcgtgc accacccgta gttc
1140
agcg tgcaggcgtt cctcgaacag gccgcccgcg acccgcacgt gctcgccatc
1200
aagcagaccc tgtaccgcac ctcgggcgac agcccggtcg tgcaggcgct gatcgacgcg
1260
gccgaagccg gcaagcaggt gctggccctc gtcgaggtga aggcccgttt cgacgaggcc
1320
aacaacatcg tctgggcacg caagctcgag aaggccggcg tgcacgtggt ctacggtctc
1380
gtcggactca agacccactg cgcc ctcgtcatcc gcgaggaaga ggggatgctg
1440
cgccactact cgcacgtcgg caccggcaac tacaacccca agaccagccg catctacgag
1500
gacttcggtc ccgc agacgcgcag gtcggcaaag acctgacacg cctgttcaac
1560
gagctcagcg gctacgcgat cgagaagaag ttcaagcgcc tgctggtcgc cccgctgcac
1620
aagg tccg ccagatcgac cgca ggaacgccga ggcggggatc
1680
cccgcgcaca tccgcatcaa ggtgaactcg atggtcgatg aggagatcat cgacgcgctc
1740
taccgcgcga gcgcggccgg ggtgaaggtc gacgtgtggg tgcgcggcat ctgcagcctg
1800
cgcaccgacc tcgacggcat cagtgacaac atcacggtgc gcagcatcct cggccgctac
1860
ctcgagcact cccgcatctt cgag aacgccggcg acccgcaggt gtacatcggc
1920
agcgccgaca accg caacctcgac cgtcgtgtgg aggcgctggt cacc
1980
gacgccgacc acctcaagga actgcaggcg ttcttcgacc tcgcgatgga cgacggaacc
2040
tcgtcgtggc atctcggcgc cggcggcgtc tgggagcgcc acgccgtgaa cgccgacggc
2100
aagccgctga tcgacctgca ggataagacc atggggttga tccagcggcg ccgccgcgcg
2160
cgggcggttc gatga
2175
<210> 9
<211> 724
<212> PRT
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIC06
<220>
<221> misc_feature
<223> SGI e ID SG1MICT849768
<220>
<221> misc_feature
<223> polyphosphate kinase
<400> 9
Met Tyr Pro Met Ile Asp Pro Ala Leu Ala Asp Ala Gly Leu Gly Asp
1 5 10 15
Ala Glu Asp Asp Asp Phe Asp Ala Ile Glu Ser Pro Asp Ser Gln Leu
25 30
Pro Asp His Arg Tyr Leu Asp Arg Glu Leu Ser Trp Leu Ala Phe Asn
40 45
Gln Arg Val Met Glu Leu Ala Glu Asp Pro Ser Leu Pro Glu Leu Glu
50 55 60
Arg Ala Asn Phe Leu Ala Ile Phe Ala Ser Asn Leu Asp Glu Phe Phe
65 70 75 80
Met Val Arg Val Ala Gly Leu Lys Arg Arg Ile Met Thr Gly Leu Ala
85 90 95
Val Pro Thr Asn Ile Gly Arg Ser Pro Val Asp Ala Leu Ala Asp Ile
100 105 110
Ser Arg Glu Ala His Ala Leu Gln Leu Arg His Ala Glu Ala Trp Thr
115 120 125
Ser Leu Val Arg Pro Ala Leu Ala Asp Ser Gly Ile Glu Ile Thr Asp
130 135 140
Trp Ser Glu Leu Thr Asp Asp Glu Arg Ser Gly Leu Ser Glu Tyr Phe
145 150 155 160
Gln Leu Gln Val Phe Pro Val Leu Met Pro Leu Ala Val Asp Pro Ala
165 170 175
His Pro Phe Pro Tyr Ile Ser Gly Leu Ser Leu Asn Leu Ala Ile Arg
180 185 190
Ile Arg Asn Ala Arg Thr Gly Arg Gln Glu Phe Ala Arg Leu Lys Val
195 200 205
Pro Pro Met Leu Pro Arg Phe Val Glu Val Pro Gly Gly Gly Glu Ile
210 215 220
Lys Arg Phe Leu Arg Leu Glu Glu Leu Ile Ala Asn His Leu Gly Asp
225 230 235 240
Leu Phe Pro Gly Met Glu Val Leu Asp His His Ala Phe Arg Leu Thr
245 250 255
Arg Asn Glu Asp Val Glu Ile Glu Glu Asp Glu Ser Glu Asn Leu Ile
260 265 270
Gln Ala Leu Glu Ala Glu Leu Leu Arg Arg Arg Phe Gly Pro Pro Ile
275 280 285
Arg Leu Glu Ile Thr Asp Asp Met Asp Glu Val Thr Met Asp Leu Leu
290 295 300
Val Arg Glu Leu Asp Ile Thr Asp Leu Glu Val Tyr Arg Leu Pro Gly
305 310 315 320
Pro Leu Asp Leu Arg Gly Leu Phe Asp Leu Ser Arg Ile Asp Arg Pro
325 330 335
Asp Leu Arg Tyr Pro Pro His Leu Pro Thr Thr Ala Val Ala Phe Gln
340 345 350
Pro Ala Gly Ser Ser Asn Arg Ala Asp Ile Phe Lys Ala Ile Arg Lys
355 360 365
Ser Asp Val Leu Val His His Pro Tyr Glu Ser Phe Thr Thr Ser Val
370 375 380
Gln Ala Phe Leu Glu Gln Ala Ala Arg Asp Pro His Val Leu Ala Ile
385 390 395 400
Lys Gln Thr Leu Tyr Arg Thr Ser Gly Asp Ser Pro Val Val Gln Ala
405 410 415
Leu Ile Asp Ala Ala Glu Ala Gly Lys Gln Val Leu Ala Leu Val Glu
420 425 430
Val Lys Ala Arg Phe Asp Glu Ala Asn Asn Ile Val Trp Ala Arg Lys
435 440 445
Leu Glu Lys Ala Gly Val His Val Val Tyr Gly Leu Val Gly Leu Lys
450 455 460
Thr His Cys Lys Leu Ala Leu Val Ile Arg Glu Glu Glu Gly Met Leu
465 470 475 480
Arg His Tyr Ser His Val Gly Thr Gly Asn Tyr Asn Pro Lys Thr Ser
485 490 495
Arg Ile Tyr Glu Asp Phe Gly Leu Phe Thr Ala Asp Ala Gln Val Gly
500 505 510
Lys Asp Leu Thr Arg Leu Phe Asn Glu Leu Ser Gly Tyr Ala Ile Glu
515 520 525
Lys Lys Phe Lys Arg Leu Leu Val Ala Pro Leu His Leu Arg Lys Gly
530 535 540
Leu Ile Arg Gln Ile Asp Ala Glu Arg Arg Asn Ala Glu Ala Gly Ile
545 550 555 560
Pro Ala His Ile Arg Ile Lys Val Asn Ser Met Val Asp Glu Glu Ile
565 570 575
Ile Asp Ala Leu Tyr Arg Ala Ser Ala Ala Gly Val Lys Val Asp Val
580 585 590
Trp Val Arg Gly Ile Cys Ser Leu Arg Thr Asp Leu Asp Gly Ile Ser
595 600 605
Asp Asn Ile Thr Val Arg Ser Ile Leu Gly Arg Tyr Leu Glu His Ser
610 615 620
Arg Ile Phe Ala Phe Glu Asn Ala Gly Asp Pro Gln Val Tyr Ile Gly
625 630 635 640
Ser Ala Asp Met Met His Arg Asn Leu Asp Arg Arg Val Glu Ala Leu
645 650 655
Val Arg Val Thr Asp Ala Asp His Leu Lys Glu Leu Gln Ala Phe Phe
660 665 670
Asp Leu Ala Met Asp Asp Gly Thr Ser Ser Trp His Leu Gly Ala Gly
675 680 685
Gly Val Trp Glu Arg His Ala Val Asn Ala Asp Gly Lys Pro Leu Ile
690 695 700
Asp Leu Gln Asp Lys Thr Met Gly Leu Ile Gln Arg Arg Arg Arg Ala
705 710 715 720
Arg Ala Val Arg
<210> 10
<211> 1390
<212> DNA
<213> Microbacterium sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIG08
<220>
<221> misc_feature
<223> encodes a 16S mal RNA
<220>
<221> misc_feature
<222> (29)..(36)
<223> n is a, c, g, t, or other
<220>
<221> misc_feature
<222> (38)..(41)
<223> n is a, c, g, t, or other
<400> 10
aacggtgaac acggagcttg ctctgtggnn nnnnnngnnn gagt aacacgtgag
caacctgccc ctgactctgg gataagcgct ggaaacggcg tctaatactg gatacgagta
gcgatcgcat ggtcagctac tggaaagatt ttttggttgg ggatgggctc gcggcctatc
agcttgttgg tgaggtaatg gctcaccaag gcgtcgacgg gtagccggcc tgagagggtg
accggccaca ctgggactga gacacggccc ctac gggaggcagc agtggggaat
attgcacaat gggcggaagc ctgatgcagc aacgccgcgt gagggatgac ggccttcggg
ttgtaaacct gcag ggaagaagcg aaagtgacgg tacctgcaga aaaagcgccg
gctaactacg cagc cgcggtaata cgtagggcgc aagcgttatc cggaattatt
gggcgtaaag agctcgtagg cggtttgtcg cgtctgctgt gaaatcccga ggctcaacct
cgggcctgca gtgggtacgg gcagactaga gtgcggtagg ggagattgga attcctggtg
tgga atgcgcagat atcaggagga atgg cgaaggcaga tctctgggcc
gtaactgacg ctgaggagcg aaagggtggg gagcaaacag gcttagatac cctggtagtc
caccccgtaa acgttgggaa ctagttgtgg ggtccattcc acggattccg tgacgcagct
aacgcattaa gttccccgcc tggggagtac ggccgcaagg ctaaaactca aaggaattga
cccg cacaagcggc ggagcatgcg gattaattcg atgcaacgcg aagaacctta
ccaaggcttg acga gaacgggcca gaaatggtca actctttgga cactcgtaaa
caggtggtgc atggttgtcg cgtg tcgtgagatg ttgggttaag tcccgcaacg
1020
agcgcaaccc tcgttctatg ttgccagcac gtaatggtgg gaactcatgg gatactgccg
1080
gggtcaactc aggt ggggatgacg tcaaatcatc atgcccctta tgtcttgggc
1140
ttcacgcatg ctacaatggc cggtacaaag ggctgcaata ccgtgaggtg gagcgaatcc
1200
gccg gtcccagttc ggattgaggt ctgcaactcg acctcatgaa gtcggagtcg
1260
ctagtaatcg cagatcagca acgctgcggt gaatacgttc ccgggtcttg tacacaccgc
1320
ccgtcaagtc atgaaagtcg cctg aagccggtgg cctt gtggagggag
1380
ccgtcgaagg
1390
<210> 11
<211> 532
<212> DNA
<213> Mycosphaerella sp.
<220>
<221> eature
<223> SGI bacterial isolate SGIH11
<220>
<221> misc_feature
<223> Internal transcribed spacer 1_5.8S ribosomal DNA
<220>
<221> misc_feature
<222> (43)..(43)
<223> n is a, c, g, or t
<220>
<221> misc_feature
<222> (526)..(526)
<223> n is a, c, g, or t
<400> 11
cggagggatc attaatgagt gagggggcca cccccaacct ccnacccttt gtgaacgcat
catgttgctt cgggggcgac gttc gcggcattcc ccccggaggt catcaaaaca
ctgcattctt acgtcggagt aaaaagttaa tttaataaaa ctttcaacaa cggatctctt
ggttctggca aaga acgcagcgaa atgcgataag taatgtgaat attc
agtgaatcat cgaatctttg aacgcacatt gcgccccctg gtattccggg gggcatgcct
gttcgagcgt catttcacca ctcaagcctc gcttggtatt gggcgtcgcg agtctctcgc
gcgcctcaaa gtctccggct gttcggttcg agcg ttgtggcaac tatttcgcag
tggagtacga gtcgtggcgg aatc tttcaaaggt tgacctcgga tcaggtaggg
atacccgctg aacttaagca tatcaataag cggaggaggt catagntgtt tc
<210> 12
<211> 1431
<212> DNA
<213> Variovorax sp.
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIG01
<220>
<221> misc_feature
<223> encodes a 16S ribosomal RNA
<400> 12
tgccttacac atgcaagtcg aacggcagcg cgggagcaat cctggcggcg agtggcgaac
gggtgagtaa tacatcggaa cgtgcccaat cgtgggggat aacgcagcga aagctgtgct
aataccgcat acgatctacg gatgaaagca ggggatcgca agaccttgcg cgaatggagc
ggccgatggc agattaggta gttggtgagg taaaggctca ccaagccttc gatctgtagc
tggtctgaga ccag ccacactggg actgagacac ggcccagact cctacgggag
gcagcagtgg ggaattttgg acaatgggcg aaagcctgat ccagccatgc cagg
atgaaggcct tcgggttgta aactgctttt gtacggaacg aaacggcctt ttctaataaa
taat accg taagaataag caccggctaa gcca gcagccgcgg
taatacgtag ggtgcaagcg ttaatcggaa ttactgggcg taaagcgtgc gcaggcggtt
atgtaagaca gttgtgaaat ccccgggctc aacctgggaa ctgt gactgcatag
ctagagtacg gtagaggggg atggaattcc gcgtgtagca tgcg tagatatgcg
gaggaacacc gatggcgaag gcaatcccct ggacctgtac tgacgctcat gcacgaaagc
gtggggagca aacaggatta gataccctgg tagtccacgc cctaaacgat gtcaactggt
gtct tcactgactc agtaacgaag ctaacgcgtg aagttgaccg cctggggagt
acggccgcaa ggttgaaact caaaggaatt gacggggacc cgcacaagcg gtggatgatg
tggtttaatt cgatgcaacg cgaaaaacct tacccacctt tgacatgtac ggaattcgcc
agagatggct tagtgctcga aagagaaccg taacacaggt gctgcatggc tgtcgtcagc
1020
cgtg agatgttggg cccg caacgagcgc tgtc attagttgct
1080
acattcagtt gggcactcta atgagactgc cggtgacaaa ccggaggaag gtggggatga
1140
cgtcaagtcc tcatggccct tataggtggg gctacacacg tcatacaatg gctggtacaa
1200
agggttgcca acccgcgagg gggagctaat cccataaaac tagt ccggatcgca
1260
gtctgcaact cgactgcgtg aagtcggaat cgctagtaat cgtggatcag aatgtcacgg
1320
tgaatacgtt tctt gtacacaccg acac catgggagcg ggttctgcca
1380
gaagtagtta gcttaaccgc aaggagggcg attaccacgg cagggttcgt g
1431
<210> 13
<211> 1424
<212> DNA
<213> Bacillus amyloliquefaciens
<220>
<221> eature
<223> SGI bacterial isolate SGIF03
<220>
<221> misc_feature
<223> encodes a 16S ribosomal RNA
<400> 13
ctggcggcgt gcctaataca tgcaagtcga gcggacagat gggagcttgc tccctgatgt
tagcggcgga cgggtgagta acacgtgggt aacctgcctg taagactggg ataactccgg
gaaaccgggg ctaataccgg atggttgtct catg gttcagacat tggc
ttcggctacc acttacagat ggacccgcgg cgcattagct agttggtgag gtaacggctc
gcga cgatgcgtag ccgacctgag agggtgatcg ctgg gactgagaca
cggcccagac tcctacggga agta gggaatcttc cgcaatggac gaaagtctga
cggagcaacg ccgcgtgagt gatgaaggtt ttcggatcgt ctgt tgttagggaa
gaacaagtgc cgttcaaata gggcggcacc ttgacggtac ctaaccagaa agccacggct
aactacgtgc cagcagccgc ggtaatacgt aggtggcaag cgttgtccgg aattattggg
cgtaaagggc tcgcaggcgg tttcttaagt ctgatgtgaa agcccccggc gggg
agggtcattg gaaactgggg aacttgagtg agga gagtggaatt ccacgtgtag
cggtgaaatg cgtagagatg tggaggaaca ccagtggcga aggcgactct ctggtctgta
actgacgctg aggagcgaaa gcgtggggag cgaacaggat tagataccct ggtagtccac
gccgtaaacg atgagtgcta agtgttaggg ggtttccgcc ccttagtgct gcagctaacg
cattaagcac tccgcctggg ggtc gcaagactga aactcaaagg aattgacggg
ggcccgcaca ggag catgtggttt aattcgaagc aacgcgaaga accttaccag
gtcttgacat cctctgacaa tcctagagat aggacgtccc cttcgggggc agagtgacag
1020
gtggtgcatg gttgtcgtca gctcgtgtcg tgagatgttg ggttaagtcc cgcaacgagc
1080
gcaacccttg atcttagttg ccagcattca cact ctaaggtgac tgac
1140
aaaccggagg aaggtgggga tgacgtcaaa tcatcatgcc ccttatgacc tgggctacac
1200
acgtgctaca atggacagaa caaagggcag cgaaaccgcg aggttaagcc aatcccacaa
1260
atctgttctc agttcggatc gcagtctgca actcgactgc gtgaagctgg aatcgctagt
1320
aatcgcggat cagcatgccg cggtgaatac gttcccgggc cttgtacaca ccgcccgtca
1380
caccacgaga aaca cccgaagtcg gtgaggtaac cttt
1424
<210> 14
<211> 1425
<212> DNA
<213> Bacillus subtilis
<220>
<221> misc_feature
<223> SGI bacterial isolate SGIH06
<220>
<221> misc_feature
<223> s a 16S ribosomal RNA
<400> 14
gctggcggcg tgcctaatac atgcaagtcg agcggacaga cttg ctccctgatg
ttagcggcgg gagt aacacgtggg taacctgcct gtaagactgg gataactccg
ggaaaccggg gctaataccg gatggttgtt tgaaccgcat ggttcagaca taaaaggtgg
cttcggctac cacttacaga tggacccgcg gcgcattagc tagttggtga ggtaacggct
caccaaggca acgatgcgta gccgacctga gagggtgatc ggccacactg ggactgagac
acggcccaga ctcctacggg aggcagcagt agggaatctt ccgcaatgga tctg
acggagcaac gccgcgtgag tgatgaaggt tttcggatcg taaagctctg ttgttaggga
agaacaagtg ccgttcaaat gcac cttgacggta cctaaccaga aagccacggc
taactacgtg ccagcagccg cggtaatacg taggtggcaa gcgttgtccg gaattattgg
gcgtaaaggg ggcg gtttcttaag tctgatgtga aagcccccgg ctcaaccggg
gagggtcatt ggaaactggg gaacttgagt gagg agagtggaat tgta
gcggtgaaat gcgtagagat gtggaggaac accagtggcg aaggcgactc tctggtctgt
aactgacgct gaggagcgaa agcgtgggga gcgaacagga ttagataccc tcca
cgccgtaaac gatgagtgct aagtgttagg gggtttccgc cccttagtgc tgcagctaac
gcattaagca ctccgcctgg ggagtacggt cgcaagactg aaactcaaag acgg
gggcccgcac tgga gcatgtggtt taattcgaag caacgcgaag aaccttacca
gaca tcctctgaca atcctagaga taggacgtcc ccttcggggg cagagtgaca
1020
ggtggtgcat ggttgtcgtc agctcgtgtc tgtt gggttaagtc ccgcaacgag
1080
cgcaaccctt gatcttagtt gccagcattc agttgggcac tctaaggtga ctgccggtga
1140
caaaccggag gaaggtgggg atgacgtcaa atcatcatgc cccttatgac ctgggctaca
1200
cacgtgctac aatggacaga acaaagggca gcgaaaccgc gaggttaagc caca
1260
aatctgttct cagttcggat cgcagtctgc aactcgactg cgtgaagctg gaatcgctag
1320
taatcgcgga tcagcatgcc gcggtgaata cgttcccggg ccttgtacac accgcccgtc
1380
acaccacgag agtttgtaac acccgaagtc ggtgaggtaa ccttt
1425
<210> 15
<211> 37
<212> DNA
<213> Artificial ce
<220>
<223> PCR primer M13-ITS1
<400> 15
tgtaaaacga cggccagttt cgtaggtgaa cctgcgg
<210> 16
<211> 38
<212> DNA
<213> Artificial ce
<220>
<223> PCR primer ITS4-M13
<400> 16
caggaaacag ctatgacctc ctccgcttat tgatatgc
<210> 17
<211> 39
<212> DNA
<213> Artificial sequence
<220>
<223> PCR primer M13-27F Bac
<400> 17
tgtaaaacga cggccagtta gagtttgatc ctggctcag
<210> 18
<211> 37
<212> DNA
<213> Artificial sequence
<220>
<223> PCR primer 1492R-M13 Bac
<400> 18
caggaaacag ctatgaccgg tgtt acgactt